For the sugar parameters you can use Glycam parameters <a href="http://glycam.ccrc.uga.edu/documents/gl_params.jsp">http://glycam.ccrc.uga.edu/documents/gl_params.jsp</a><br>After with specific script it can be convert to Gromac readable file:<br>
<a href="http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software">http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software</a><br><br>I hope it would be useful for you.<br>
<br>Rasoul<br><div class="gmail_quote">On Wed, Aug 18, 2010 at 6:45 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
Jianhui Tian wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Parichita,<br>
<br>
Thanks for the suggestion. However, the question is what parameters from ffG53a6 can be used for not included sugars or glycolipid. I guess you can not simply use the charge, angle and dihedral values based on the atom types from 53a6.<br>
<br>
</blockquote>
<br></div>
Gromos building blocks are quite transferable between different molecules. Compare a few sugars - the parameters are nearly identical. That is one of the central features of this particular force field, that functional group charges should be as versatile as possible.<br>
<br>
As for the lipids, there are new versions of 53A6 (which I believe have been uploaded to the Gromacs site) that perform substantially better than the built-in parameters. The long acyl chains are not particularly accurate in the default 53A6.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
Jianhui<br>
<br>
Date: Wed, 18 Aug 2010 16:18:49 +0530 (IST)<br></div>
From: parichita parichita <<a href="mailto:parichitamajumdar@yahoo.co.in" target="_blank">parichitamajumdar@yahoo.co.in</a> <mailto:<a href="mailto:parichitamajumdar@yahoo.co.in" target="_blank">parichitamajumdar@yahoo.co.in</a>><div class="im">
<br>
><br>
Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6<br></div>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>><br>
Message-ID: <<a href="mailto:456742.75700.qm@web8903.mail.in.yahoo.com" target="_blank">456742.75700.qm@web8903.mail.in.yahoo.com</a> <mailto:<a href="mailto:456742.75700.qm@web8903.mail.in.yahoo.com" target="_blank">456742.75700.qm@web8903.mail.in.yahoo.com</a>>><div class="im">
<br>
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 for small molecules in PDB format (or simple text structures) to the following topology formats: GROMOS, GROMACS and from literature if you can find out the parameters of ffG53a6 force field, then you can correct the charge, angle and dihedral values that you are collected from the PRODRG. Hope this will help you.<br>
Regards...<br>
Parichita...........<br>
<br>
<br>
<br>
Parichita Mazumder 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></div>
--- On Wed, 18/8/10, Jianhui Tian <<a href="mailto:jianhuitian@gmail.com" target="_blank">jianhuitian@gmail.com</a> <mailto:<a href="mailto:jianhuitian@gmail.com" target="_blank">jianhuitian@gmail.com</a>>> wrote:<br>
<br>
<br>
From: Jianhui Tian <<a href="mailto:jianhuitian@gmail.com" target="_blank">jianhuitian@gmail.com</a> <mailto:<a href="mailto:jianhuitian@gmail.com" target="_blank">jianhuitian@gmail.com</a>>><div class="im"><br>
Subject: [gmx-users] carbohydrate parameters in ffG53a6<br></div>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><div class="im"><br>
Date: Wednesday, 18 August, 2010, 10:16 AM<br>
<br>
<br>
Hi,<br>
<br>
I want to do some simulations about carbohydrates and glycolipid. In the ffG53a6.rtp file, I just see limited parameters for carbohydrate, like monosaccharide Glucose, Mannose and Galactose. What parameters can be used for others like arabinose? Also, is there any parameters available in the Gromacs force field for glycolipid?<br>
<br>
Jianhui<br>
<br>
</div></blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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