[gmx-users] pdb2gmx gives topol.top without values for bonds angles and dihedrals.

David Saez davidsaezsan at gmail.com
Wed Dec 25 00:04:59 CET 2013

Dear all, I want to create a topology for S-adenosylmethionine using
AMBER99SB force field. I had to create some new atomtypes and, accordingly,
I have modified all the necessary files (atomtypes.atp, ffbonded,
ffnonbonded, etc). When I make 

pdb2gmx -f sam.pdb

I obtain a topol.top describing correctly the charges, and the atoms forming
the bonds, angles, etc. generated from the data I introduced in the rtp
entry. My problem is that file doesn't show the values of the force
constants, bond lengths, etc. It looks like pdb2gmx were succesfully reading
rtp entry but were not looking into ffbonded.itp:

I wonder if the problem is because this a standalone residue, (not forming
part of a chain). Below you can see what th eTerminal shows when I type
pdb2gmx -f sam.pdb

If some one can tell me what I am doing wrong I am going to be very
I wish you a merry christmas.

David Saez S.

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