From sunil.patel from camcellnet.com Mon Jun 2 07:13:58 2008 From: sunil.patel from camcellnet.com (Sunil Patel) Date: Mon Jun 2 11:00:38 2008 Subject: [Molecular-modelling] Re: Molmodel Digest, Vol 20, Issue 3 In-Reply-To: <200805311704.m4VH4TO19910@net.bio.net> References: <200805311704.m4VH4TO19910@net.bio.net> Message-ID: <859405740806020513o61a06e29o4aaf8669e29d300b@mail.gmail.com> Hi Vladimir , The problem with docking inorganic molecules into protein structures is with at atom typing ie Charges to be placed on the atoms..fully charged, partial charges. Most forcefields are either biased to proteins or inorganic molecules and metals. There is no comprehensive forcefield that covers all. You will need to check the forcefield library for the atoms and molecules covered. In general people approximate the charges. Run the expts, see if the molecule is distorted. Rerun expts to overcome after charge modifications for adjusting the distortions. regards, Sunil. On 31/05/2008, molmodel-request@oat.bio.indiana.edu < molmodel-request@oat.bio.indiana.edu> wrote: > > Send Molmodel mailing list submissions to > molmodel@net.bio.net > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bio.net/biomail/listinfo/molmodel > or, via email, send a message with subject or body 'help' to > molmodel-request@net.bio.net > > You can reach the person managing the list at > molmodel-owner@net.bio.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Molmodel digest..." > > > Today's Topics: > > 1. Re: inorganic mol. docking (Vladimir Petrov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 30 May 2008 18:16:04 -0400 > From: Vladimir Petrov > Subject: [Molecular-modelling] Re: inorganic mol. docking > To: molmodel@net.bio.net > Message-ID: > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > X-no-archive: yes > sudha.mrig@gmail.com wrote: > > I want to dock an inorganic molecule like ZnSO4, MgOAc etc. with a > > protein molecule. > > I guess, you'd have to familiarize yourself with basics of General > Chemistry first, and then decide how to dock ZnSO4 "in organic molecule" > into the protein structure... > > > ------------------------------ > > _______________________________________________ > Molmodel mailing list > Molmodel@net.bio.net > http://www.bio.net/biomail/listinfo/molmodel > > End of Molmodel Digest, Vol 20, Issue 3 > *************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.bio.net/bionet/mm/molmodel/attachments/20080602/45859d28/attachment.html From yellowish from gmail.com Mon Jun 9 13:04:49 2008 From: yellowish from gmail.com (Protenger) Date: Mon Jun 9 15:25:21 2008 Subject: [Molecular-modelling] Lattice vs Off-Lattice models Message-ID: Hi all I just have a simple question. What is the deffernce(s) between lattice and off-lattice models in protein folding simulations. Thank you