From owner-molec-model@net.bio.net Tue Dec 01 22:00:00 1998 From: "clive delmonte" Newsgroups: bionet.biophysics,bionet.xtallography,bionet.molec-model Subject: DNA Structure: Puzzle Number 5 Date: Wed, 2 Dec 1998 08:10:34 -0000 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: 195.7.227.213 Message-ID: <3665733a.0@news.netdirect.net.uk> X-Trace: 2 Dec 1998 17:04:58 GMT, 195.7.227.213 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!amsterdam1-snf1!news.gtei.net!diablo.theplanet.net!dispose.news.demon.net!demon!ayres.ftech.net!news.ftech.net!peer.news.nildram.co.uk!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.227.213 Lines: 53 Xref: biosci bionet.biophysics:4612 bionet.xtallography:4504 bionet.molec-model:2336 The Crystallographers' Paradox Several teams of crystallographers have reported on the interconversion of the B to the Z form under very mild conditions inside solid fibres of drawn DNA (26,27), as well as the B to D form conversion under similar, very mild conditions (28) The very mild conditions are interpreted by some (27,28) to mean that the B and Z forms, and the B and D forms, respectively, must have the same helical handedness. (Another team (26) seems to offer no interpretation of their observation of the B to Z transition inside a fibre.) The reversible conversion inside fibres of the A to, and from, the B form has been known for many years, and therefore the A, B, D and Z forms would all seem to have the same helical handedness. However, there are many studies of diffraction from true oligonucleotide crystals which purport to show that the A and B forms are right-handed, for example (29,30), and purport to show that the Z form is left-handed, for example (31). How can all the crystallographers be right ? 26 Polymorphism of DNA Double Helices; A.G.W. Leslie, S. Arnott, R. Chandrasekaran & R.L. Ratliff; J Mol Biol Vol 143 (1980) 49 - 72 27 B to Z Transition in a DNA Fibre: The Question of Handedness of the Duplex; V. Sasisekharan & S.K. Brahmachari; Current Science Vol 50 (1981) 10 - 13 28 Time-resolved X-ray Diffraction Studies of the B to D Structural Transition in the DNA Double Helix; A. Mahendrasingham, V.T. Forsyth, R. Hussain, R.J. Greenall, W.J. Pigram & W. Fuller; SCIENCE Vol 233 (1986) 195 - 197 29 Conformation of d(GGGATCCC) x 2 in crystals and in solution studied by X-ray diffraction, Raman spectroscopy and molecular modelling; H. Fabian, W. Holzer, U. Heinemann, H. Sklenar & H. Welfle; Nucleic Acids Research Vol 21 (1993) 569 - 576 30 Crystal Structure Analysis of a Complete Turn of B-DNA; R. Wing, H. Drew, T. Takano, C. Broka, S. Tanaka, K. Itakura & R.E. Dickerson; Nature Vol 287 (1980) 755 - 758 31 Molecular Structure of a Left-handed Double Helical DNA Fragment at Atomic Resolution; A.H.-J. Wang, G.J. Quigley, F.J. Kolpak, J.L. Crawford, J.H. van Boom, G. van der Marel & A. Rich; Nature Vol 282 (1979) 680 - 686 -------------------------------------------------------------------------- Clive Delmonte From owner-molec-model@net.bio.net Wed Dec 02 22:00:00 1998 From: "clive delmonte" Newsgroups: bionet.biophysics,bionet.molec-model,bionet.xtallography Subject: DNA Structure: Puzzle Number 6 Date: Thu, 3 Dec 1998 07:37:37 -0000 Lines: 50 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: 195.7.227.194 Message-ID: <3666bd28.0@news.netdirect.net.uk> X-Trace: 3 Dec 1998 16:32:40 GMT, 195.7.227.194 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.cwix.com!194.72.7.126!btnet-peer!btnet!news.freedom2surf.net!peer.news.nildram.co.uk!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.227.194 Xref: biosci bionet.biophysics:4614 bionet.molec-model:2337 bionet.xtallography:4505 Leslie et al.(Puzzle 5, re. 26) reported that a fibre of poly(dI).poly(dC), which gave sharp X-ray diffraction spots shortly after being drawn, was unstable and transformed irreversibly after a few days into poly(dC).poly(dI).poly(dC+). This new, three-stranded molecule also gave sharp spots in its own X-ray diffraction pattern which did not have any of the original spots. Therefore the conversion was complete. Very similar results had been reported for fibres of poly(dA).poly(dT) converting to poly(dT).poly(dA).poly(dT) (9) and for the formation of poly(U).poly(A).poly(U) from poly(U).poly(A) (10). The problem is evident: How and where would the torque arise inside a solid fibre that would permit one double helix to rotate so as to unwind one strand and rewind it onto an adjacent triple helix having a different diameter and rotating at a different angular velocity ? Inside the fibre, individual molecules would have a random axial translation so only very rarely would two adjacent double helices have the same axial starting point down the fibre, and they would be unlikely to be perfectly straight inside the fibre but would probably be entwined around neighbours. How would there be a very high conversion of double to triple stranded molecules when any rotation of adjacent double helices would normally find the free ends of one of them axially displaced down the fibre compared to its neighbour ? 9 Structures for the Polynucleotide Complexes Poly(dA).Poly(dT) & Poly(dT).Poly(dA).Poly(dT); Struther Arnott & E. Selsing; J Mol Biol Vol 88 (1974) 509-521 10 Structures for Poly(U).poly(A).poly(U) Triple Stranded Polynucleotides; Struther Arnott & P.J. Bond; Nature New Biology Vol 244 (1973) 99-101 ------------------------------------------------------------------ Clive Delmonte From owner-molec-model@net.bio.net Thu Dec 03 22:00:00 1998 From: "clive delmonte" Newsgroups: bionet.biophysics,bionet.molec-model Subject: DNA Structure: Puzzle Number 7 Date: Thu, 3 Dec 1998 19:14:55 -0000 Lines: 43 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: 195.7.225.147 Message-ID: <36680781.0@news.netdirect.net.uk> X-Trace: 4 Dec 1998 16:02:09 GMT, 195.7.225.147 Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cpk-news-hub1.bbnplanet.com!news.gtei.net!newsfeed.cwix.com!194.72.7.126!btnet-peer!btnet!news.freedom2surf.net!peer.news.nildram.co.uk!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.225.147 Xref: biosci bionet.biophysics:4616 bionet.molec-model:2338 McGhee & Felsenfeld (12) reacted nucleosomal DNA with dimethyl sulphate and recorded their surprise at their results: "We are unable to detect any significant difference between the reactivity of the N7 of guanines in nucleosomal DNA and of that in naked DNA... Contrary to our expectation, there is no detectable periodic modulation of reactivity corresponding to the twist of DNA on the nucleosome surface... Judging from the relative concentration of intact unreacted DNA remaining, the guanines in the nucleosome reacted about 20 - 30% FASTER (their emphasis) than in the isolated DNA... " For a double helix, about half the DNA wrapped around a nucleosome core should lie on the inside in contact with the histone proteins, or up against adjacent turns of the DNA and therefore offer reduced accessibility to methylation. Crucially, the double helix offers no clue as to how the methylation of nucleosomal DNA could be faster than it is for naked DNA. There is a clue in the true side-by-side structure found by Lee et al. (Puzzle 1, ref. 1). With the base pairs linked directly across the sugar-phopsphate chains, and stacked upon each other, all the base pairs would be equally exposed to the methylating reagent. The reaction could be faster when wound onto nucleosomal cores because there would be no folding up of the DNA, which would obstruct the approach of the reagent, as is found in DNA in solution. 12 Reaction of Nucleosomal DNA with Dimethyl Sulfate; J.D. McGhee & G. Felsenfeld; Proc. Nat. Acad. Sci. (USA) Vol 76 (1979) 2133 - 2137 ------------------------------------------------------------ Clive Delmonte From owner-molec-model@net.bio.net Sun Dec 06 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Cutie85523@aol.com Newsgroups: bionet.molec-model Subject: Photo Mousepads ....... Great Christmas Gifts ! Date: 7 Dec 1998 10:10:23 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 160 Message-ID: <74g9if$2hi$1@mserv2.dl.ac.uk> NNTP-Posting-Host: mserv2.dl.ac.uk content-length: 3699 Return-Path: Apparently-To: GREAT CHRISTMAS GIFT IDEA! PHOTO TRANSFER SPECIALTIES! MOUSEPADS WITH YOUR FAVORITE PHOTOS! Now you can have your favorite photos printed onto mousepads! 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From owner-molec-model@net.bio.net Sun Dec 06 22:00:00 1998 From: "clive delmonte" Newsgroups: bionet.biophysics,bionet.molec-model Subject: DNA Structure: Puzzle Number 8 Date: Sun, 6 Dec 1998 17:21:50 -0000 Lines: 42 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: 195.7.227.191 Message-ID: <366be1d1.0@news.netdirect.net.uk> X-Trace: 7 Dec 1998 14:10:25 GMT, 195.7.227.191 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!btnet-peer!btnet-feed2!btnet!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.227.191 Xref: biosci bionet.biophysics:4624 bionet.molec-model:2340 Mirzabekov et al. (13) reported their study of the sequence in which nucleosomal histones are brought into contact with DNA wrapped around nucleosomal core proteins. They observed that the first 20 bp of both 5' ends of the DNA are not in close association with any core histones even though the 3' ends, paired with those same 5' ends which are not in any contact, are indeed in close association with parts of histones H2A and H3. How would it be, in a double helix with 2 full turns in the last 20 bp at each end, that only the 3' ends, but not the 5' ends, would lie in close association with core histones ? There is a clue the true side-by-side structure found by Lee et al. (Puzzle 1, ref.1), and found by other STM & AFM workers. If the 5' end of the duplex twists away from the nucleosome surface in order to prepare to make contact with the next nucleosome, then it could be only the 3' end alone which is left in contact with the histones. What other explanation could one suggest ? 13 Primary Organisation of Nucleosome Core Particle of Chromatin: Sequence of Histone Arrangement Along DNA; A.D. Mirzabekov, V.A. Shick, A.V. Belyavsky & S.G. Bavykin; Proc. Nat. Acad. Sci. (USA) Vol 75 (1978) 4184 - 4188 ---------------------------------------------------- Clive Delmonte From owner-molec-model@net.bio.net Mon Dec 07 22:00:00 1998 From: "clive delmonte" Newsgroups: bionet.biophysics,bionet.molec-model,bionet.xtallography Subject: DNA Structure: Puzzle Number 9 Date: Mon, 7 Dec 1998 11:56:13 -0000 Lines: 78 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: 195.7.227.182 Message-ID: <366ce70c.0@news.netdirect.net.uk> X-Trace: 8 Dec 1998 08:45:00 GMT, 195.7.227.182 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!btnet-peer!btnet!news.freedom2surf.net!peer.news.nildram.co.uk!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.227.182 Xref: biosci bionet.biophysics:4627 bionet.molec-model:2341 bionet.xtallography:4509 Suwalski & Traub (14) studied a fibre of the DNA-polyarginine complex by X-ray diffraction. Their diffraction pattern shows "pronounced streaks" in a hexagonal lattice of side 4.15nm and they remarked that the equatorial reflections followed h x h + h x k + k x k = 3n. This pattern of equatorial presences is equivalent to that of Fuller et al. (Puzzle Number 4, ref.6) where such presences follow h-k=3n in a cell whose side can be reduced. Squaring (h-k) and subtracting from the expression in the previous paragraph, there is a differerence of 3hk, a quantity always divisible by 3. Therefore Suwalski & Traub's value of 'a' can reduced by root 3. Suwalski and Traub decided that their pattern of systematic absence could be explained by postulating axial translations of the molecules equal to c/3. Marvin et al. (Puzzle Number 4, ref. 5) considered that a random axial translation of their molecules of c/2 would account for the streaks on their layer lines. Now, the very same diffraction pattern of Suwalski and Traub with DNA-polyarginine was reindexed on an orthogonal net by Fita et al. (15) in a unit cell of approximate section 2.6nm x 3.6 nm (16) where equatorial reflections followed h+k=2n. Langridge et al. (Puzzle Number 4, ref. 7) have shown that this pattern of presences would allow the halving of the long side of the cell section. Fita et al. considered that the pattern of systematic absences in their orthogonal net indicated that the axial translation of the molecules was c/4. So Suwalski & Traub considered that the fibre had axial displacements of the molecules of c/3 in a hexagonal net, and Fita et al. found the axial displacement to be c/4 in an orthogonal net. But there was only one single fibre and only one diffraction pattern. Therefore, whether a hexagonal or orthogonal array is chosen, the axial dispacement can only have one value. The value common to both analyses is c/2, but this is deducible from the layer line streaks and not from the patterns of systematic absence. Therefore the patterns of systematic absence in both the hexagonal and orthogonal nets should be taken to show that, for both indexing schemes, a smaller unit cell is the right choice, with a random axial displacement of c/2. However, if the unit cell sizes are reduced accordingly, the double helix can no longer be fitted into the reduced dimensions of the original cells. As we have seen in the earlier Puzzles, a true side-by-side duplex, where each helix has a diameter of about 1.3nm, and, in this case, has its grooves at least partially filled with poly-arginine, will fit the new, reduced unit cells. 14 A Comparative X-ray Study of a Nucleoprotamine & DNA Complexes with Polylysine & Polyarginine; M. Suwalski & W. Traub; Biopol. Vol 11 (1972) 2223 - 2231 15 X-ray Diffraction Study of DNA Complexes with Arginine Peptides and Their Relation to Nucleoprotamine Structure; I. Fita, J.L. Campos, L.C. Puigjaner & J.A. Subirana; J Mol Biol Vol 167 (1983) 157 - 177 16 X-ray Diffraction Studies of Nucleoprotamine Structure; P. Suau & J.A. Subirana; J Mol Biol Vol 117 (1977) 909 - 926 --------------------------------------------------------------------- Clive Delmonte From owner-molec-model@net.bio.net Wed Dec 09 22:00:00 1998 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.cwix.com!204.186.110.126!ptdnetP!newsgate.ptd.net!news.cc.ukans.edu!not-for-mail From: PGegen@UKans.nolospamare.edu (Dr. Peter Gegenheimer) Newsgroups: bionet.molec-model Subject: Re: DNA Structure: Puzzle Number 9 Date: 10 Dec 1998 16:20:46 GMT Organization: Univ. Kansas (BCMB) Lines: 42 Message-ID: <7opiGDf98QgB-pn2-9eNUrjIYcHdV@rnaworld.bio.ukans.edu> References: <366ce70c.0@news.netdirect.net.uk> Reply-To: PGegen@UKans.nolospamare.edu NNTP-Posting-Host: rnaworld.bio.ukans.edu Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable X-Newsreader: ProNews/2 Version 1.00 On Mon, 7 Dec 1998 11:56:13, "clive delmonte" wrote: > Suwalski & Traub (14) studied a fibre of the DNA-polyarginine complex by > X-ray diffraction. Their diffraction pattern shows "pronounced streaks" in > a hexagonal lattice of side 4.15nm and they remarked that the equatorial > reflections followed h x h + h x k + k x k =3D 3n. > > This pattern of equatorial presences is equivalent to that of Fuller et al. > (Puzzle Number 4, ref.6) where such presences follow h-k=3D3n in a cell whose > side can be reduced. Squaring (h-k) and subtracting from the expression in > the previous paragraph, there is a differerence of 3hk, a quantity always > divisible by 3. Therefore Suwalski & Traub's value of 'a' can reduced by > root 3. > > As we have seen in the earlier Puzzles, a true side-by-side duplex, where > each helix has a diameter of about 1.3nm, and, in this case, has its grooves > at least partially filled with poly-arginine, will fit the new, reduced unit > cells. --SNIP-- *Please* do NOT cross-post this to bionet.molec-model. It has zero to do with molecular modelling! It bothers me when, seeing that there are some new posts to this little-used group, and eagerly opening my newsreader's folder in hope of some new information, I find that there is just some erudite spam. (I.e., one person's intellectual meat is another's Spam(R).) Thanks! PG o----------------------------------------------------------------------o | Dr. Peter Gegenheimer | Vox: 785-864-3939 FAX: 785-864-5321 | | Department of | PGegen@UKans.nospam.edu | | Molecular Biosciences | http://rnaworld.bio.ukans.edu/ | | & Dept. Evol Biology | | | University of Kansas |"When you have excluded the impossible, | | 2045 Haworth Hall | whatever remains, however improbable, | | Lawrence KS 66045-2106 | must be the truth." S. Holmes | o_____________________________|________________________________________o From owner-molec-model@net.bio.net Thu Dec 10 22:00:00 1998 Path: biosci!SLIP.NET!grizzly From: grizzly@SLIP.NET (Michael Sherrell) Newsgroups: bionet.molec-model Subject: ACT 396 for sale Date: 10 Dec 1998 20:20:28 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 14 Sender: daemon@net.bio.net Distribution: world Message-ID: <01BE247A.013C6D60@oak-pm2-1-193.dialup.slip.net> NNTP-Posting-Host: net.bio.net For sale: 1998 Advanced Chemtech Model 396 Multiple Biomolecular Synthesizer, unused, ~2/3 of new price. Also available: Perkin Elmer Sciex API III+ LC/MS/MS, electrospray, APCI, $79,000 Hewlett Packard 5989B LC/MS, electrospray, extend mass range, 1995 model, $45,000 Plus many ABI and other sequencers and synthesizers (and service arrangements for synthesizers), flow cytometers, NMRs and SEMs listed on my website. Michael Sherrell Grizzly Analytical 707 887 2919/fax 707 887 9834 www.grizzlyanalytical.com From owner-molec-model@net.bio.net Thu Dec 10 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!netnews.com!newspeer.monmouth.com!rill.news.pipex.net!pipex!server1.netnews.ja.net!pegasus.csx.cam.ac.uk!not-for-mail From: Yu Wai Chen Newsgroups: bionet.molec-model Subject: modelling peptide/protein with solvents Date: Fri, 11 Dec 1998 13:55:02 +0000 Organization: MRC Centre for Protein Engineering Lines: 19 Message-ID: <36712436.590EA71F@mrc-lmb.cam.ac.uk> NNTP-Posting-Host: ind4.mrc-lmb.cam.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=big5 Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 4.5C-SGI [en] (X11; I; IRIX64 6.4 IP30) X-Accept-Language: zh-TW, zh-CN, en Dear experts, I am thinking of studying the effect of water (if possible, entropic effects) on the secondary structure of a peptide/protein of about 100 residues. Can you suggest what programs are best suited to this purpose? I am especially interested in those that are for free academic use because my project is one off. Can you also briefly tell me what hardware is required? Thanks a lot. -- =================================================================== Yu Wai CHEN, Ph.D. .................. email: ywc@mrc-lmb.cam.ac.uk Centre for Protein Engineering, tel: 44-(1223) 402148 MRC Centre, Cambridge CB2 2QH, U.K. fax: 44-(1223) 402140 WWW homepage: http://www.mrc-cpe.cam.ac.uk/people/wai.html From owner-molec-model@net.bio.net Sat Dec 12 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!192.232.20.2!malgudi.oar.net!hyperion.wright.edu!news.wright.edu!not-for-mail From: Deacon Sweeney Newsgroups: bionet.molec-model Subject: Re: modelling peptide/protein with solvents Date: Sun, 13 Dec 1998 01:23:18 -0500 Organization: Wright State University Lines: 372 Message-ID: <36735D56.41C6@wright.edu> References: <36712436.590EA71F@mrc-lmb.cam.ac.uk> NNTP-Posting-Host: linus.bmb.wright.edu Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------167E2781446B" X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP30) CC: ywc@mrc-lmb.cam.ac.uk This is a multi-part message in MIME format. --------------167E2781446B Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I think that AMBER is about the best you can do inexpensively. AMBER is a suite of programs designed to allow groups to perform molecular dyamic simulations, and to analyze the results of such simulations. It does offer solvation options, both box and droplet. What do you mean entropic effects? sweeney.2@wright.edu www.amber.ucsf.edu/amber/amber.html I think we got it for a few hundred dollars. Best wishes, Deacon Sweeney Wright State University Yu Wai Chen wrote: > > Dear experts, > > I am thinking of studying the effect of water (if possible, entropic > effects) on the secondary structure of a peptide/protein of about 100 > residues. > > Can you suggest what programs are best suited to this purpose? I am > especially interested in those that are for free academic use because my > project is one off. Can you also briefly tell me what hardware is > required? > > Thanks a lot. > > -- > =================================================================== > Yu Wai CHEN, Ph.D. .................. email: ywc@mrc-lmb.cam.ac.uk > Centre for Protein Engineering, tel: 44-(1223) 402148 > MRC Centre, Cambridge CB2 2QH, U.K. fax: 44-(1223) 402140 > WWW homepage: http://www.mrc-cpe.cam.ac.uk/people/wai.html --------------167E2781446B Content-Type: text/html; charset=us-ascii; name="amber.html" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="amber.html" Content-Base: "http://www.amber.ucsf.edu/amber/amber. html" AMBER

Welcome to AMBER

image of amber with a trapped bug

"All the bugs are not out of Amber"

What is AMBER?

Assisted Model Building with Energy Refinement

AMBER refers to two things: a molecular mechanical force field for the simulation of biomolecules (which is in general use in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. The current version of this package is AMBER ver 5 which is sold for UCSF by Oxford Molecular, subject to a licensing agreement as described below. The code is written in Fortran and C and requires approximately 65 megabytes of disk space.

AMBER is developed in an active collaboration of Peter Kollman and the Kollman group at UCSF, Dave Case at The Scripps Research Institute, Ken Merz at Penn State, David Ferguson at the University of Minnesota, Tom Darden at NIEHS, and Dave Pearlman at Vertex Pharmaceuticals.

AMBER information

How to obtain the current version of AMBER?

AMBER5 is now available exclusively from OXFORD MOLECULAR.

If you are interested in obtaining a copy of AMBER 5.0, please contact Oxford Molecular at one of the following sites: 

         USA:
                   Toll Free:  1-800-876-9994
                   phone (408) 879-6300   fax (408) 879-6302
                   e-mail: products@oxmol.com


         UK:       phone  +44 1865 784600 fax +44 1865 784601
                   e-mail:  products@oxmol.co.uk

General correspondence

 Please direct specific correspondence about AMBER (including queries about maintenance, bugs etc.) to:
    amber-request@cgl.ucsf.edu

Currently this mail goes to caldwell@cgl.ucsf.edu (Jim Caldwell). General queries should be addressed to the Oxford Molecular support addresses.

UCSF contact information:

School of Pharmacy, Attention: Willa Crowell
Department of Pharmaceutical Chemistry
University of California
San Francisco, California 94143-0446
(415) 476-1540
FAX: (415) 476-0688
email: willa@cgl.ucsf.edu

The AMBER Mail Reflector

 One of the best sources of information about running and understanding AMBER is the AMBER Mail Reflector.

The Mail Reflector exists to provide a forum for discussions on the use of the AMBER software and for release of bugfixes. Mail reflectors distribute mail sent to the reflector address to all subscribers to the reflector list.

To join/unjoin the reflector, send e-mail to:

    amber-request@cgl.ucsf.edu
To post or mail to the list, e-mail to:
    amber@cgl.ucsf.edu

Please use this list for discussion of AMBER-specific issues only; in particular, announcements of general interest to the online chemistry community should be sent to the community's main reflector, CHEMISTRY@ccl.osc.edu. AMBER users are encouraged to join this list too - MAILSERV@ccl.osc.edu: HELP CHEMISTRY for info. The CHEMISTRY reflector may also be a good place to send requests for new force field parameters, since many other programs use the Weiner et al. and Cornell et al. force fields.

The AMBER programs

 The release consists of about 65 programs, with 930 source files containing over 332,000 lines, of which about 187,000 lines are code. The code has traditionally been all FORTRAN, but with the 4.1 release, 30% of the code is in C (LEaP is 20% of the total). The release is managed under UNIX; the UNIX version as distributed contains all the management tools, including the ability to generate source code for non-UNIX systems and utilities for e.g. recursive ftp of a source tree to VMS machines. All versions include all the source code. The major programs are as follows:
  • sander: Simulated annealing with NMR-derived energy restraints. This allows for NMR refinement based on NOE-derived distance restraints, torsion angle restraints, and penalty functions based on chemical shifts and NOESY volumes.

  • gibbs: This program includes free energy perturbation (FEP) and thermodynamic integration (TI) [window growth, slow growth, and dynamically modified windows], and also allows potential of mean force (PMF) calculations.

  • roar: This module was contributed by Ken Merz' group at Penn State. It allows mixed quantum-mechanical/molecular-mechanical (QM/MM) calculations, "true" Ewald simulations, and alternate molecular dynamics integrators.

  • spasms: San Francisco Package of Applications for the Simulation of Molecular Systems. An alternative molecular dynamics code distributed with AMBER.

  • nmode: Normal mode analysis program using first and second derivative information, used to find search for local minima, perform vibrational analysis, and search for transition states.

  • prep, edit, link, parm: Routines to create AMBER coordinate and parameter/topology input files. NOTE: This functionality is duplicated in AMBER with the release of LEaP (the old programs are also included in the release).

  • LEaP: LEaP is an X-windows-based program that provides for basic model building and AMBER coordinate and parameter/topology input file creation. It includes a molecular editor which allows for building residues and manipulating molecules. Example xleap windows (40Kbytes of gifs). Motif-style X-windows Athena widgets and a table widget used in LEaP were written by Vladimir Romanovski.

  • Interface: `Interface' is a scripting language that can be used for running Sander and Gibbs with higher-level input specifications. It includes various intrinsic functions such as DO-loops, IF and GOTO constructs, variable assignment statements, numerous functions (e.g. SIN, COS, EXP, etc.), and in-line variable substitution. Thus, one can run numerous AMBER jobs from one script, changing only desired elements of the simulation for each run. For example, one might define a torsional restraint whose target value changed on each iteration of a DO-loop. This makes it easy to perform torsional driving, for example.

  • Other programs include nucgen for building model DNA structures, anal, mdanal and carnal for structure analysis, and other programs...
    Please see the AMBER manuals for more information.

Compilation / platform independence

 A compilation system has been devised for FORTRAN that allows the user to compile everything in two steps on any version of UNIX by copying a single file (called the MACHINE file) containing machine dependencies from a library covering about 22 types of UNIX, then running a script which invokes about 50 Makefiles. The same system allows source code to be generated for VMS, VM/CMS, DOS, and CTSS operating systems. Unlike the source code, this compilation system has been placed in the public domain. Latest Machine.* platform files

The MACHINE file sets UNIX environment variables which define compiler commands for various optimization levels as well as various flags which are used by the cpp preprocessor to screen each FORTRAN source file for machine dependencies (including shared memory and message-passing parallelism), which are delimited with ``#ifdef ... #endif'' constructs. Cpp also handles ``#include'' statements, which are typically used for common blocks.

The MACHINE environment variables are used by a shell script (Compile) which is invoked by the Makefiles to compile and link the FORTRAN programs or to generate target source for a given machine. The MACHINE file also indicates a machine-specific directory where a library, sys.a, is built, which can include basic C library routines such as getarg() to be linked with FORTRAN if the machine's FORTRAN library is deficient. A small library of machine-dependent FORTRAN routines is provided: mexit() allows the programs to return success/failure status to the operating system; amopen() hides variations in open(); and second() and wall() hide details of cpu and wallclock timing.

For more information, see General correspondence above.

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With close to 100 newsgroups to run, the BIOSCI staff has to rely on the discussion leaders of each newsgroup to report problems directly to us at biosci-help@net.bio.net. We will moderate any of our newsgroups if the discussion leader tells us that the readership of the group wishes to do so and if a moderator is willing to do the work. For most BIOSCI/bionet groups, this entails only a few minutes of work each day. Moderating a newsgroup will resolve probably 95% of the junk postings on the USENET distribution. Unfortunately there are easy ways for determined spammers to override the moderation mechanism on USENET, but we can protect our e-mail subscribers from unwanted postings if the newsgroup is moderated. You can also access our newsgroups over the WWW at URL http://www.bio.net. While this Web interface will not stop spammers from trying to post to the groups, this will give you yet another way, besides using USENET news, to keep the junk out of your personal mail files. For those of you with local USENET news systems, the Web interface will also give you faster access to new newsgroups and recent postings. 3) Examples of subscribing and unsubscribing to the mailing lists. ------------------------------------------------------------------ PLEASE NOTE: The BIOSCI management does NOT act on subscription/unsubscription requests that are posted improperly to the newsgroups and mailing lists. People who do this only bother everyone on the lists to no avail. Please be sure to follow the proper procedures below. Gory details are in the BIOSCI Information sheets on the Web at http://www.bio.net. 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From owner-molec-model@net.bio.net Sat Dec 26 22:00:00 1998 Path: biosci!bloom-beacon.mit.edu!news.kodak.com!news-nysernet-16.sprintlink.net!news-east1.sprintlink.net!news-peer-europe.sprintlink.net!news.sprintlink.net!Sprint!newsfeed1.swip.net!swipnet!news-fra.maz.net!news-lond.gip.net!news-stkh.gip.net!news.gsl.net!gip.net!news.kolumbus.fi!not-for-mail From: "Seeker" Newsgroups: alt.sex.wanted.models,alt.sf.scale-models,alt.supermodels,alt.supermodels.cindy-crawford,alt.tv.models-inc,asu.research.modelling,aus.rail.models,bionet.molec-model,de.rec.modelle.bahn,de.rec.modelle.misc,fj.rec.models Subject: HELP! Who is this model? Date: Sun, 27 Dec 1998 14:25:16 +0200 Lines: 351 Message-ID: <76594t$h6c$1@news.kolumbus.fi> NNTP-Posting-Host: m136m3hel.dial.kolumbus.fi X-Newsreader: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Anybody knows the name of this model (unforgettable77@(dontwritethis)yahoo.com) begin 666 00001.jpg M_]C_X `02D9)1@`!`0```0`!``#_VP!#``@&!@<&!0@'!P<)"0@*#!0-# L+ M#!D2$P\4'1H?'AT:'!P@)"XG("(L(QP<*#P`!,>])<>4D M`@G':FE/*<3 $>U-*?(&TC% 2ET$[BH\=:Z7W$CTF)ZS0*G03 -<4LK)SZ10 M./.D`29^M,)4IPQ)CK25J^PIUIO\HF8H""XEH>6#(VCBA+E92PGO.(IU*2,Y MD8H>Y(4$@=Z!;"R8628[4ZZ[YG7%"H!""F]0$B% M#-11$*5^E VN20D&O ;01NBELC>2?YATKBMH7&PR>]!R8/-)*@3BE%*@?Y2: M6"$P0)/44"(P",&FE@A1G@TXM1VSB2>M-;A,\QR:!M2P#S3*U)/29I3BD$X' MJ[FJ]XB\2,Z6/(9*7+@B2.B?G0&:CJMOIC'F/JB<)2,E1["JG<^*-4N5E-LR MS;H4?25Y4?O5:>U&XN7E..N%2E&9/2B+%;27T.+4I2IZC'[B@E%:AKC@#CEV MXM*3E+:=L_8"B3XD3:M(3:L... 2Y^)2"%?;/ZU+,ZNA+97"GPD`[0T&TQV$ M$F?<14 XDWMPM3+$/3,.D@)]^Q^M`V\SJ&LO&]M;,6J3\10["/I)G]30R=/U M!I\H=7*=P$[I"I[4*ZS?W5R6V_-><)B&P3)]@*]>:7J^G;1>,/6YY2EP[3]J M`ERWU!N[_(4\%,C<,G(GI]ZMZ+\M+MD7FYOSFT+0HCTG<,?+((^E4>VUJ^M% M[@Z2=NT$Y@586-4_UT6Z'UH2ZE:4A/$I"BJ /G'WH+8'BG^7Y5SR91N4J">E M<*RA(;)E0'[4XGU1N5MCF@:\I*4XR>M)5!68^$<44^4@I"! 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YI)1*0>(]Z9<8V MYB@&*HY^U(*MOSI:D%1C@4P\=B8H--T>_+VFVSY.Y2D"?GP:E'+M)]4`=ZJW MA=<^'&%*SZE#]35@MDH7A0DF@4NXX)'IKC;BG$DIPF>]>> 0F DGM%#H405) M. #TH"E2N1,D"8IA8$^JDA6 4\^]-.K6D@1%!<=6:)=<\L"0:B"VM$[A)(X- M6"_=2JY<],]XJ+?X&T0(@T$IEBX"5 *P?>H30RAG0+5LCU%,_K:6,I4 M4FKR\XN3ZC574 N]<4KG>:"2M]J&@8BB!)'%(0D!)2.*XTHJ&30=6HA)!Z4$ MZ<<9HUS*:!<(0">O2C7_BJ/?\`]P^W% R3.>M>B'PT" M:X.:77 D30>S2IKW>NCI\Z!0,BEH(!I"0,4L`30.*(,&:6CBFATI]($4#B!F MI"W1@?M0#?(J4MTB!]* QI)51*QM3$4TQS7GE&#]*!EU05R8,YBHYVV"WD^Y MS19Y-)/Q)/7%!-L7J4H2@8"1`^0HC\6%)DQ-0!41P:<0ZLS)H)QJ]"3 _6GV M[J2F1UJ!;<5)SUHMAQ04!,B>M!8+=X%1]\T\EYLD^N%=<5$)<4A0VF/E74RI '1DG[T'__V0`` ` end From owner-molec-model@net.bio.net Mon Dec 28 22:00:00 1998 Path: biosci!daresbury!not-for-mail From: Success@dl.ac.uk Newsgroups: bionet.molec-model Subject: Attention Insurance Agents and Financial Planners -15798 Date: 29 Dec 1998 09:04:29 -0000 Organization: Daresbury Laboratory, Warrington, U.K. Lines: 40 Message-ID: <76a5ut$9c4$1@mserv2.dl.ac.uk> NNTP-Posting-Host: mserv2.dl.ac.uk Original-To: Agents@dl.ac.uk content-length: 343 Return-Path: Attention Insurance Agents and Financial Planners Would you like to retire in 5 years making all the money you want. Whether you are a professional or newcomer, there is something you have been missing until now. More Info Call 800 607-6006 Ex 2493# then go to 1 to hear about opportunity. Thank You From owner-molec-model@net.bio.net Mon Dec 28 22:00:00 1998 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.maxwell.syr.edu!newsfeed.cwix.com!192.232.20.2!malgudi.oar.net!hyperion.wright.edu!news.wright.edu!not-for-mail From: Deacon Sweeney Newsgroups: bionet.molec-model Subject: MD simulations? Date: Tue, 29 Dec 1998 13:09:44 -0500 Organization: Wright State University Lines: 13 Message-ID: <36891AE8.167E@wright.edu> NNTP-Posting-Host: linus.bmb.wright.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP30) Hello, I am a college sophmore, quite interested in proteins and molecular dynamics. In order to enhance my educational experience, I think that it would be wise for me to look at a variety of molecular dynamics simulations of proteins in water. If you have any, or know where I could find any databases, please contact me at sweeney.2@wright.edu My ultimate aim is to work against the deteriorating effects of age on the human nervous system. Thanks in advance, Deacon Sweeney Wright State University From owner-molec-model@net.bio.net Mon Dec 28 22:00:00 1998 Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!newsfeed1.swip.net!swipnet!rill.news.pipex.net!pipex!server1.netnews.ja.net!news.nottingham.ac.uk!not-for-mail From: Benny Lo Newsgroups: bionet.molec-model Subject: Insight/Discover/Fix Residues Date: Tue, 29 Dec 1998 16:14:01 +0000 Organization: ACS, The University of Nottingham Lines: 16 Message-ID: <3688FFC9.41C6@holmes.cancres.nottingham.ac.uk> NNTP-Posting-Host: marple.cancres.nottingham.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Trace: oyez.ccc.nottingham.ac.uk 914948122 22677 128.243.118.200 (29 Dec 1998 16:15:22 GMT) X-Complaints-To: usenet@news.nottingham.ac.uk NNTP-Posting-Date: 29 Dec 1998 16:15:22 GMT X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) Dear All I tried to use the Discover module within Insight (MSI) to minimize a protein I have built using homologous structures. Before I started the minimization, I fixed the positions of certain residues using Constraint/Fix. However, I found that these residues aren't actually saved when I save the whole folder and I have to key in all these two hundred odd residues next time I want to repeat the procedure. Does anyone know how I can make the program remember these residues to be fixed in minimization? Thank you for your help. Please email to: benny@holmes.nott.ac.uk Rgds B. Lo From owner-molec-model@net.bio.net Wed Dec 30 22:00:00 1998 Path: biosci!YAHOO.COM!nvs7849 From: nvs7849@YAHOO.COM Newsgroups: bionet.molec-model Subject: about your site Date: 30 Dec 1998 20:40:02 -0800 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 75 Sender: daemon@net.bio.net Distribution: world Message-ID: <199812310439.UAA28908@net.bio.net> NNTP-Posting-Host: net.bio.net We'll Submit Your Site To Over 900 Search Engines, Directories, & Indices For A "One Time Cost" Of Only $ 39.95 *** 100% Money Back Guarantee *** *** Immediately Increase Your Sites Exposure *** For Less Than 4 Cents Each We Will Submit Your Web Site To Over 900 Of The Net's Hottest Search Engines, Directories & Indices. If your site isn't listed in the Search Engines, how can people find you to buy your products or services? For just $39.95 we'll take the work load off your back instead of you trying to do it manually which can take days to do. 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