Hi Justin,<br><br>I compare the few sugars (Glc, Gal, Man), their parameters are indeed nearly identical except for some improper dihedrals.<br>Then I can transfer these parameters to other sugars.<br>How about Glycolipid? For example, the link "phosphatidyl-myo-inositol". Do you have any suggestion? <br>
Thanks.<br><br>Jianhui<br><br>Date: Wed, 18 Aug 2010 12:45:15 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
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Jianhui Tian wrote:<br>
> Hi Parichita,<br>
><br>
> Thanks for the suggestion. However, the question is what parameters from<br>
> ffG53a6 can be used for not included sugars or glycolipid. I guess you<br>
> can not simply use the charge, angle and dihedral values based on the<br>
> atom types from 53a6.<br>
><br>
<br>
Gromos building blocks are quite transferable between different molecules.<br>
Compare a few sugars - the parameters are nearly identical. That is one of the<br>
central features of this particular force field, that functional group charges<br>
should be as versatile as possible.<br>
<br>
As for the lipids, there are new versions of 53A6 (which I believe have been<br>
uploaded to the Gromacs site) that perform substantially better than the<br>
built-in parameters. The long acyl chains are not particularly accurate in the<br>
default 53A6.<br>
<br>
-Justin<br>
<br>
> Jianhui<br>
><br>
> Date: Wed, 18 Aug 2010 16:18:49 +0530 (IST)<br>
> From: parichita parichita <<a href="mailto:parichitamajumdar@yahoo.co.in">parichitamajumdar@yahoo.co.in</a><br>
> <mailto:<a href="mailto:parichitamajumdar@yahoo.co.in">parichitamajumdar@yahoo.co.in</a>><br>
> ><br>
> Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6<br>
> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><div id=":5f">><br>
> Message-ID: <<a href="mailto:456742.75700.qm@web8903.mail.in.yahoo.com">456742.75700.qm@web8903.mail.in.yahoo.com</a><br>
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> Content-Type: text/plain; charset="iso-8859-1"<br>
><br>
> Hi Jianhui,<br>
> For your sugar part you can use PRODRG, which will convert coordinates<br>
> for small molecules in PDB format (or simple text structures) to the<br>
> following topology formats: GROMOS, GROMACS and from literature if you<br>
> can find out the parameters of ffG53a6 force field, then you can<br>
> correct the charge, angle and dihedral values that you are collected<br>
> from the PRODRG. Hope this will help you.<br>
> Regards...<br>
> Parichita...........<br>
><br>
><br>
><br>
><br>
> Parichita Mazumder<br>
> Research Fellow<br>
> C/O Dr. Chaitali Mukhopadhayay<br>
> Department of Chemistry<br>
> University of Calcutta<br>
> 92,A P C Road<br>
> Kolkata-700009<br>
> India.<br>
><br>
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