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.
http://www.gromacs.org/Documentation/Tutorials
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.
-Justin
Thanks any help is welcome
Henri
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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