[gmx-users] Re: Re: Re: Glucose Ring transition

[Patel Ronak Y]

Dear Dr Spoel,

I used nrexcl=3. I think it should be correct. I tried eleminating some of
the intramolecular interactions of glucose ring but the problem persists.

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.

> Date: Fri, 28 Jan 2005 16:27:42 +0530 (IST)
> From: "Patel Ronak Y" <ronakp at iitb.ac.in>
> Subject: [gmx-users] Re: gmx-users Digest, Vol 9, Issue 51
> To: gmx-users at gromacs.org
> Message-ID: <36838.10.124.5.106.1106909862.squirrel at gpo.iitb.ac.in>
> Content-Type: text/plain;charset=iso-8859-1
>
> 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.