[gmx-users] Merging two topology files

Naser, Md Abu mn2 at hw.ac.uk
Thu Oct 13 14:30:51 CEST 2005

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?

With regards,


> 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 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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