From owner-molmodel@hgmp.mrc.ac.uk  Mon Mar 11 16:50:43 2002
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From: eawilder@yahoo.com (Elizabeth)
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Subject: InsightII H-bonding question
Date: 11 Mar 2002 08:46:00 -0800
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Greetings,

I am trying to use MSI InsightII to do MD studies on some small
sugar-like gelators.  I would like to be able to monitor
intermolecular hydrogen-bonding throughout the simulation, but I'm not
sure if, or how, I can do this.  I started out just modeling a few
molecules in a cell and had planned to monitor the distances between
the hydrogen bonding sites, but this isn't a great way to do it, and
furthermore with the PBC, sometimes one of the molecules will start to
interact with a "neighbor" instead of the other molecules, which
defeats the purpose of my distance monitors.  If anyone has any
suggestions or advice for someone new to MD, I would be most
appreciative.

Thanks.


From owner-molmodel@hgmp.mrc.ac.uk  Thu Mar 14 16:06:31 2002
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From owner-molmodel@hgmp.mrc.ac.uk  Thu Mar 14 16:06:42 2002
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From: maillist@cruizn.co.za ("Africatravelsearch Mailing List")
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Subject: Its Indaba  time again.
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From owner-molmodel@hgmp.mrc.ac.uk  Fri Mar 15 06:35:57 2002
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Subject: GET FREE PORN ACCESS NOW!!          pqonpfinCphu/dmq1phu...pqonpn53;Bkpng2ero...
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From owner-molmodel@hgmp.mrc.ac.uk  Tue Mar 26 23:36:32 2002
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From: "Yuyuan Guo" <yuyuan@students.wisc.edu>
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Subject: ECL
Date: Tue, 26 Mar 2002 17:05:30 -0800
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Hi, Friends:

Do you know which company produce ECL substrate? I am working on western
blot.

Thanks for your suggestion.

Peter



From owner-molmodel@hgmp.mrc.ac.uk  Tue Mar 26 23:36:35 2002
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From: "Yuyuan Guo" <yuyuan@students.wisc.edu>
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Subject: restrict enezyme
Date: Tue, 26 Mar 2002 16:54:57 -0800
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Dear Friends:

I have cloned one gene into TA vector. The ORF was with ClaI and SalI on
both ends. With specific primers, I can do PCR to amplify the gene from the
plasmid. This means the gene is in the plasmid. However, when I used ClaI
and SalI to cut the ORF, I could not get the band that is 1.1kb of the gene.

I tried other plasmid with other ORF with same vector and same restrict
enzyme ends, I can get the band.

As ClaI is methylation sensitive, I transform the plasmid into 110 meth(-)
E.coli.

Could it be that the primer was mis-formed? Like I order CCG, but they
formed CTG. So the restrict site is changed.

How do you think?

Thanks.

Peter



From owner-molmodel@hgmp.mrc.ac.uk  Fri Mar 29 19:36:34 2002
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From: webmaster@softberry.com
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Subject: GETATOMS: Computing side chain conformations by simulated annealing
Date: 29 Mar 2002 19:35:50 -0000
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  GETATOMS: Computing side chain conformations by simulated annealing 
     with frozen main chain atoms is release as one of new program in 
         protein structure prediction suit: sspal, nnssp, ssenvid
            (3D-comp, FOLD and H-model will appear soon also):

                         Available at www.softberry.com

              http://www.softberry.com/berry.phtml?topic=prot_new&prg=GETATOMS

GETATOMS is a program of modelling atomic coordinates of a protein with unknown 
3D structure.It uses main chain coordinates from 3D structure of similar 
protein, which sequence is aligned with a query protein. Restoration of loops 
in alignment will be added later. 
GETATOMS also has an option to provide coordinates of H-atoms.

GETATOMS computes 3D protein coordinates of a query protein and estimate 
quality of produced 3D structure using several scores: 

Steric_Score a la JMB (1997), 267, 1268-1282 
VDW_Score a la JMB(1981) v.153,p.1087-1109 
and Bump Score is number of atomic pairs having sterically forbiden overlap. 
Resulting 3D structure can be visualized using 3D-viewers such as RasMol.

INPUT is PDB structure of similar protein with known 3D structure and alignment 
query sequence and template protein sequence in several formats.

For example if we have 4hhb (A) sequence as query 1hba(B) as template: 
Simple format:

      VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDL------SHGSAQVKGHGKKVAD
      HLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPRTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG

      ALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVST
      AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN

      VLTSKYR
      ALAHKYH


--------------------------------------------------------------------------------

GETATOMS output:
      HEADER    OXYGEN TRANSPORT                        07-MAR-84   4HHB    
      REMARK  50
      REMARK  50 GETATOMS [ver=0.9.0.0; date=20020312]
      REMARK  50 Modelled from template structure provided by user.
      REMARK  50 Calculation parameters:
      REMARK  50   Simulated Annealing Temperature=2.000000
      REMARK  50   Simulated Annealing Maximal number of steps=100
      REMARK  50   Simulated Annealing steps done=-1073216864
      REMARK  50   Add Hydrogen Atoms=OFF
      REMARK  50 Final score data:
      REMARK  50   VDW_Score=1.089206e-19
      REMARK  50   Steric_Score=2.652495e-315
      REMARK  50   Bump_Score=0.000000e+00
      ATOM      1  N   VAL     1       9.223 -20.614   1.365
      ATOM      2  CA  VAL     1       8.694 -20.026  -0.123
      ATOM      3  C   VAL     1       9.668 -21.068  -1.645
      ATOM      4  O   VAL     1       9.370 -22.612  -0.994
      ATOM      5  CB  VAL     1       8.948 -18.511  -0.251
      ATOM      6  CG1 VAL     1       8.554 -18.010  -1.636
      ATOM      7  CG2 VAL     1       8.176 -17.751   0.822
      ATOM      8  N   LEU     2       9.270 -20.650  -2.180
      ATOM      9  CA  LEU     2      10.245 -21.378  -3.143

      or  WITH H-atoms:

      REMARK  50   Add Hydrogen Atoms=ON
      REMARK  50 Final score data:
      REMARK  50   VDW_Score=1.089206e-19
      REMARK  50   Steric_Score=2.652495e-315
      REMARK  50   Bump_Score=0.000000e+00
      ATOM      1  N   VAL     1       9.223 -20.614   1.365
      ATOM      2  CA  VAL     1       8.694 -20.026  -0.123
      ATOM      3  C   VAL     1       9.668 -21.068  -1.645
      ATOM      4  O   VAL     1       9.370 -22.612  -0.994
      ATOM      5  CB  VAL     1       8.948 -18.511  -0.251
      ATOM      6  CG1 VAL     1       8.554 -18.010  -1.636
      ATOM      7  CG2 VAL     1       8.176 -17.751   0.822
      ATOM      8 1H   VAL     1      10.102 -20.497   1.435
      ATOM      9 2H   VAL     1       8.812 -20.175   2.021
      ATOM     10 3H   VAL     1       9.034 -21.482   1.426
      ATOM     11  HA  VAL     1       9.166 -20.592  -0.926
      ATOM     12  HB  VAL     1      10.006 -18.305  -0.091
      ATOM     13 1HG1 VAL     1       9.071 -17.073  -1.845
      ATOM     14 2HG1 VAL     1       8.833 -18.752  -2.384
      ATOM     15 3HG1 VAL     1       7.477 -17.846  -1.671
      ATOM     16 1HG2 VAL     1       7.168 -17.540   0.463
      ATOM     17 2HG2 VAL     1       8.120 -18.356   1.727
      ATOM     18 3HG2 VAL     1       8.686 -16.814   1.043
      

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