[gmx-users] g_rotacf create tpr from pdb

Justin A. Lemkul jalemkul at vt.edu
Sat Aug 14 17:23:21 CEST 2010

henri mone wrote:
> Dear Gromacs experts and newbies,
> The program "g_rotacf" (calculates the autocorrelation function)
> requires as input for the -s option either a "tpr", "tpb" or "tpa"
> file.
> I does not accept for the -s option a PDB file :- ( .
> How can I create from a "pdb" file a "tpr" file?
> The program "pdb2gmx" can only create from a  "pdb a "top" or  "gro"
> file but no "tpr" file.
> I also tried "grompp" but this needs a "mdp" file.
> Making it short here are my two questions:
> 1. How do I create for "g_rotacf" a  "tpr", "tpb" or "tpa" file?

Please consult any basic tutorial to get a grasp for a basic Gromacs workflow.


> 2. "g_rotacf" only extracts the coordinates from the xtc trajectory
> why does it need a topology file (via  "tpr", "tpb" or "tpa").

Probably because it needs some type of information not stored in .pdb files - 
bonds, masses, PBC information, etc.


> Thanks any help is welcome
> Henri


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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