[gmx-users] HYP GROMOS

[Abil Aliev]

Hello,

Thank you for your response.

The topology file was propared using pdb2gmx. I changed one of the improper dihedral angles (CG-CD-CB-O) for HYP to (CG-CD-O-CB) and CG of HYP stopped inverting. 

There seems to be much less of proper dihedrals in the topology file on using pdb2gmx for GROMOS force fields compared to OPLS-AA or AMBER. For example, for the OPLS-AA there are 3 dihedrals in the topology around the N-CA bond:

C(i-1) - N - Ca - Ha
C(i-1) - N - Ca - C
C(i-1) - N - Ca - Cb

Following the same logic, there should be two dihedrals in the GROMOS topology file, but there is only one (C(i-1) - N - Ca - C). Any special reason for this?

Abil

----------------------------------------
> Date: Sun, 19 Oct 2008 10:52:13 +0200
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] HYP GROMOS
> 
> Abil Aliev wrote:
>>   Hello,
>> 
>> I have done calculations using standard GROMOS 43a1 and 53a6 parameters 
>> (GROMACS 3.3.3) for a 4-hydroxy-L-proline derivative (HYP), where the 
>> gamma-OH and the alpha-CO groups are trans to each other in the starting 
>> structure. However, over the course of MD the trans-configuration of 
>> these two substituents changes into a cis-configuration, which was not 
>> supposed to happen. Is there any way to avoid such isomerisation?
>> 
> Dihedral potentials, maybe you need to add an improper...
>> Abil
>> 
>> 
>> 
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>> 
>> 
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> 
> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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