[gmx-users] Re: Re: Re: Re: Glucose ring transition
Patel Ronak Y
ronakp at iitb.ac.in
Tue Feb 1 08:07:47 CET 2005
Dear Dr Spoel,
The problem of glucose ring transition is fixed.
Some proper ring dihedrals (defined with respect to other ring carbons) I
replaced with dihedrals defined with repect to exocyclic groups
Thanks for your suggestions.
> Message: 6
> Date: Mon, 31 Jan 2005 02:51:01 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Re: Re: Re: Glucose Ring transition
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1107136261.5676.13.camel at vangogh>
> Content-Type: text/plain
> On Mon, 2005-01-31 at 10:35 +0530, Patel Ronak Y wrote:
>> Dear Dr Spoel,
>> I used nrexcl=3. I think it should be correct. I tried eleminating some
>> the intramolecular interactions of glucose ring but the problem
>> Once againg I would like to mention is that for galactose and N-acetyl
>> galactosamine, the chair coformation is nicely maintained. In galactose
>> hydroxyl group at C4 is axial and for glucose it is equatorial,
>> configuration of all other carbons is same.
>> Out of six torsions of glucose ring three are absolutely fine but other
>> three are skewed up.
> Obviously the correct conformation is still subject to large forces. Try
> to find out where they come from by doing an energy minimization and
> look at the individual energy terms. It is easy to define impropers
> incorrectly, but ther could also be a pair interaction that should be
> turned off.
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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