[gmx-users] Merging two topology files

[David van der Spoel]

On Thu, 2005-10-13 at 13:30 +0100, Naser, Md Abu wrote:
> Thanks David for your response.
> 
> I have decane water interface and protein is solvated in water phase
> of the system.
> I am using GROMOS-96 for protein and GROMACS force field for  decane
> which is actually provided by you.
> I started off with decane to make susre that I have a correct density
> using GROMACS force field
> and then I have protein topoly of GORMOS-96 using pdb2gmx. I managed
> to build the system using genbox.
> I believe ther sould not be any problem using this approach. All I
> need to figure out how to merge these two topology files.
> Any suggestions?
Apart from physically merging them which is described in CH. 5 of the
manual, you need to find appropriate atom types for the decane in the
GROMOS force field. That should just be CH2 and CH3.

> 
> With regards,
> 
> Abu
> 
> 
> 
> > Hi All,
> >
> > I have two topology files of two different force fields. I am having
> > problems with merging them. Can anyone advise me regarding the
> > problem?
> This is generally not a good idea, unless you have positive evidence
> otherwise. But please provide more info. What kind of topologies?
> 
> 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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-- 
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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