On Sat, Aug 28, 2010 at 8:11 PM, Justin A. Lemkul <[email protected]> wrote:
> > > Rasoul wrote: > > >> >> On Thu, Aug 19, 2010 at 1:02 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> Rasoul wrote: >> >> 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 >> >> >> Mixing and matching force field parameters is a very bad idea. To >> have a valid >> physical model, parameters should be derived in compatible ways. >> >> It has good consistency with Amber FF :J Comput Chem 29: 622–655, 2008. >> >> > That's exactly what it was designed to do, which I don't question. But the > OP was attempting to develop united-atom parameters for use with Gromos96 > 53A6. For clarity, I pointed out that mixing GLYCAM and 53A6 is an incorrect > notion. > > Amber and Glycam FF can be imported to Gromacs and this method I think has a more lower artificiality. -Justin > Rasoul > > -Justin >> > >> Rasoul >> >> I hope it would be useful for you. >> >> Rasoul >> On Wed, Aug 18, 2010 at 6:45 PM, Justin A. Lemkul >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[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]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>> >> >> > >> Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6 >> To: Discussion list for GROMACS users >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> <mailto:[email protected] >> >> <mailto:[email protected]> >> >> <mailto:[email protected] >> <mailto:[email protected]>>>> >> Message-ID: <[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[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]> >> <mailto:[email protected] >> <mailto:[email protected]>> <mailto:[email protected] >> >> <mailto:[email protected]> >> >> <mailto:[email protected] >> <mailto:[email protected]>>>> wrote: >> >> >> From: Jianhui Tian <[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> <mailto:[email protected] >> >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>>> >> >> Subject: [gmx-users] carbohydrate parameters in ffG53a6 >> To: [email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> <mailto:[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 <http://vt.edu> <http://vt.edu> | (540) >> >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> <mailto:[email protected] <mailto:[email protected]>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[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] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > 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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