Hi Justin, I compare the few sugars (Glc, Gal, Man), their parameters are indeed nearly identical except for some improper dihedrals. Then I can transfer these parameters to other sugars. How about Glycolipid? For example, the link "phosphatidyl-myo-inositol". Do you have any suggestion? Thanks.
Jianhui Date: Wed, 18 Aug 2010 12:45:15 -0400 From: "Justin A. Lemkul" <[email protected]> Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6 To: Discussion list for GROMACS users <[email protected]> Message-ID: <[email protected]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed 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. >
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