[gmx-users] Re: gmx-users Digest, Vol 9, Issue 51

[David van der Spoel]

On Fri, 2005-01-28 at 16:27 +0530, Patel Ronak Y wrote:
> Dear Dr Spoel,
> 
> I use ffG43a1 force field. I prepared rtp file for sugar building blocks.
> This file contains only atoms (type,charge,charge groups), bonds and
> improper dihedral angle.
> 
> I left the generation of proper dihedrals and non-bonding parameters on
> GROMACS.I don't exclude any pair for non-bonding parameters that generated
> by GROMACS.

check your pairs and nrexcl (see chapters 4&5 of manual)
> 
> Thanks.
> 
> > Date: Fri, 28 Jan 2005 07:39:38 +0100
> > From: David <spoel at xray.bmc.uu.se>
> > Subject: Re: [gmx-users] Problem with Glucose ring
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <1106894378.5726.1.camel at studio.bibu>
> > Content-Type: text/plain
> >
> > On Fri, 2005-01-28 at 11:27 +0530, Patel Ronak Y wrote:
> >> Dear Gromacs users.
> >>
> >> I have prepared sugar topology files for galactose, N-acetyl
> >> galactosamine
> >> GalNAc) and glucose. I have carried out some simulations.
> >>
> >> The problem that occurs is, during simulations the Glucose ring
> >> conformation (chair conformation) get skewed up. The Galactose and
> >> GalNAc
> >> nicely maintain the chair conformation.
> >>
> >> I have checked topology files many and many times, I have plotted angle,
> >> dihedrals, improper dihedrals also. Everything seem to be fine and
> >> around
> >> equilibrium values.
> >>
> >> An interesting thing to note is that galactose and glucose varies only
> >> at
> >> C4 position. In my simulations, the galactose ring is stable in chair
> >> conformation and glucose ring is in somewhat skewed chair conformation.
> >> Can somebody give suggestion what might be the reason?
> 
> > Check the pairs and the number of exclusions. Maybe there is large
> > exclusion inside the molecule. If your dihedrals are correct you could
> > even just turn off intramolecular interactions altogether. You didn't
> > say what force field you used.
> 
> >>
> >> --------------------------------------------------------------------------
> >> Patel Ronak Y.
> >> School of Bioscience and Bioengineering,
> >> Indian Institute of Technology Bombay,
> >> Mumbai-400076
> >> Maharashtra
> >> India.
> >>
> >> --------------------------------------------------------------------------
> 
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-- 
David.
________________________________________________________________________
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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