[gmx-users] Merging several topology files

[Shang-Te Danny Hsu]

Dear listers,

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 
that?
2) If so, how do I convert them into suitable formats with the 
coordinate file and the topology file?

best regards,
Danny
-- 
Shang-Te Danny HSU
Department of NMR Spectroscopy
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht, the Netherlands
phone: +31-30-2539931 | fax: +31-30-2537623
e-mail: hsu at nmr.chem.uu.nl