<br><br><div class="gmail_quote">On Thu, Aug 19, 2010 at 1:02 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>
Rasoul wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
For the sugar parameters you can use Glycam parameters <a href="http://glycam.ccrc.uga.edu/documents/gl_params.jsp" target="_blank">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" target="_blank">http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software</a><br>
<br>
</blockquote>
<br></div>
Mixing and matching force field parameters is a very bad idea. To have a valid<br>
physical model, parameters should be derived in compatible ways.<br>
<br></blockquote><div>It has good consistency with Amber FF :J Comput Chem 29: 622–655, 2008.<br><br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
-Justin<br>
<br></blockquote><div>Rasoul <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<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">
I hope it would be useful for you.<br>
<br>
Rasoul<br></div><div><div></div><div class="h5">
On Wed, Aug 18, 2010 at 6:45 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
Jianhui Tian wrote:<br>
<br>
Hi Parichita,<br>
<br>
Thanks for the suggestion. However, the question is what<br>
parameters from ffG53a6 can be used for not included sugars or<br>
glycolipid. I guess you can not simply use the charge, angle and<br>
dihedral values based on the atom types from 53a6.<br>
<br>
<br>
Gromos building blocks are quite transferable between different<br>
molecules. Compare a few sugars - the parameters are nearly<br>
identical. That is one of the central features of this particular<br>
force field, that functional group charges should be as versatile as<br>
possible.<br>
<br>
As for the lipids, there are new versions of 53A6 (which I believe<br>
have been uploaded to the Gromacs site) that perform substantially<br>
better than the built-in parameters. The long acyl chains are not<br>
particularly accurate in the 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" target="_blank">parichitamajumdar@yahoo.co.in</a><br>
<mailto:<a href="mailto:parichitamajumdar@yahoo.co.in" target="_blank">parichitamajumdar@yahoo.co.in</a>><br>
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<mailto:<a href="mailto:parichitamajumdar@yahoo.co.in" target="_blank">parichitamajumdar@yahoo.co.in</a>>><br>
<br>
><br>
Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div></div>
<mailto:<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>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</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<br>
coordinates for small molecules in PDB format (or simple text<br>
structures) to the following topology formats: GROMOS, GROMACS<br>
and from literature if you can find out the parameters of<br>
ffG53a6 force field, then you can correct the charge, angle and<br>
dihedral values that you are collected from the PRODRG. Hope<br>
this will help you.<br>
Regards...<br>
Parichita...........<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><div class="im">
--- On Wed, 18/8/10, Jianhui Tian <<a href="mailto:jianhuitian@gmail.com" target="_blank">jianhuitian@gmail.com</a><br></div>
<mailto:<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>
<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><br></div>
<mailto:<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><br>
<mailto:<a href="mailto:jianhuitian@gmail.com" target="_blank">jianhuitian@gmail.com</a>>>><br>
<br>
Subject: [gmx-users] carbohydrate parameters in ffG53a6<br>
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>><br>
<mailto:<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>
<br>
Date: Wednesday, 18 August, 2010, 10:16 AM<br>
<br>
<br>
Hi,<br>
<br>
I want to do some simulations about carbohydrates and<br>
glycolipid. In the ffG53a6.rtp file, I just see limited<br>
parameters for carbohydrate, like monosaccharide Glucose,<br>
Mannose and Galactose. What parameters can be used for others<br>
like arabinose? Also, is there any parameters available in the<br>
Gromacs force field for glycolipid?<br>
<br>
Jianhui<br>
<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></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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>
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<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>
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