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. I wish you a merry christmas. David Saez S. -- View this message in context: http://gromacs.5086.x6.nabble.com/pdb2gmx-gives-topol-top-without-values-for-bonds-angles-and-dihedrals-tp5013521.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.