[gmx-users] Merging several topology files

David van der Spoel spoel at xray.bmc.uu.se
Wed Dec 12 22:09:34 CET 2001

On Wed, 12 Dec 2001, Shang-Te Danny Hsu wrote:

>I am currently trying to build a topology file for an unusual 
>biomolecule wich has more than 200 atoms. Due to the size limitation of 
>the PRODRG server, I made several topology files as the fragments of the 
>whole molecule. By comparing the overlapped region, I glued/merged these 
>fragments together into a complete topology file.However, I still have 
>some questions about the format of the topology files.
>1) Because of the minimization, the coordinates of the overlapped 
>fragments moved slightly. Would that be okay to merge them together like 
>2) If so, how do I convert them into suitable formats with the 
>coordinate file and the topology file?
I don't think this approach will work. The problem is that you get
nonbonded interactions between the fragment. If you want to merge these it
will have to be in one molecule, but this means you have to renumber
everything and your topology becomes useless.

You can try to use x2top, which has no size limits but which is relatively
stupid... It may also crash in the current version...

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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