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

[Patel Ronak Y]

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.

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.
>>
>> --------------------------------------------------------------------------