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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On Apr 25, 2012, at 8:02 PM, colvin <colvin4367.gmail.com> wrote: > Hi, > > Thanks for the reply, but my prmtop file is actually generated from > chamber, i cannot use ambpdb to get pdb file because it gives me > error: ERROR: Flag "TITLE" not found in PARM file. Is there any other > workaround? > > Thanks and regards, > Colvin > > > > On Wed, Apr 25, 2012 at 8:26 PM, David A Case <case.biomaps.rutgers.edu> wrote: >> On Wed, Apr 25, 2012, colvin wrote: >>> >>> From the previous entry in amber archive, i came to know about this >>> program, add_pdb that add residue and atom information to the prmtop >>> file. I tried it and it did added in %FLAG RESIDUE_number in the new >>> prmtop file. I then used this new prmtop file to generate a pdb file, >>> (by traj in inpcrd file and traj out pdb) but the output pdb file does >>> not come with the original residue numbering, and it is numbered from >>> 1. >> >> Ptraj doesn't know anything about the extra sections in the prmtop file. >> Use ambpdb with the "-ext" flag to convert a prtmop/inpcrd file pair >> into a pdb file, making use of the extra information. >> >> ....dac >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Apr 25 2012 - 17:30:11 PDT