For the sugar parameters you can use Glycam parameters http://glycam.ccrc.uga.edu/documents/gl_params.jsp After with specific script it can be convert to Gromac readable file: http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software
I hope it would be useful for you. Rasoul On Wed, Aug 18, 2010 at 6:45 PM, Justin A. Lemkul <[email protected]> wrote: > > > Jianhui Tian wrote: > >> Hi Parichita, >> >> 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. >> >> > 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. > > 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. > > -Justin > > Jianhui >> >> Date: Wed, 18 Aug 2010 16:18:49 +0530 (IST) >> From: parichita parichita <[email protected] <mailto: >> [email protected]> >> >> > >> Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6 >> To: Discussion list for GROMACS users <[email protected] <mailto: >> [email protected]>> >> Message-ID: <[email protected] <mailto: >> [email protected]>> >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi Jianhui, >> 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. >> Regards... >> Parichita........... >> >> >> >> Parichita Mazumder Research Fellow >> C/O Dr. Chaitali Mukhopadhayay >> Department of Chemistry >> University of Calcutta >> 92,A P C Road >> Kolkata-700009 >> India. >> >> --- On Wed, 18/8/10, Jianhui Tian <[email protected] <mailto: >> [email protected]>> wrote: >> >> >> From: Jianhui Tian <[email protected] <mailto:[email protected]>> >> >> Subject: [gmx-users] carbohydrate parameters in ffG53a6 >> To: [email protected] <mailto:[email protected]> >> >> Date: Wednesday, 18 August, 2010, 10:16 AM >> >> >> Hi, >> >> 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? >> >> Jianhui >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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