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

Justin Lemkul jalemkul at vt.edu
Wed Dec 25 01:50:04 CET 2013

On 12/24/13, 6:04 PM, David Saez wrote:
> 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
> grateful.

There is nothing wrong.  For the AMBER, CHARMM, and OPLS force fields, there are 
no values explicitly printed to the .top file.  They are looked up in 
ffbonded.itp when grompp is executed; if something is missing (i.e. not found in 
the force field), it triggers a fatal error.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


More information about the gromacs.org_gmx-users mailing list