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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On Apr 26, 2012, at 4:39 AM, colvin <colvin4367.gmail.com> wrote: > Hi, > > Thank you for the reply. I can now use ambpdb with the vmd compatible > chamber prmtop. > > Is there a way for ptraj to recognise the extra section in the prmtop > file? if i need to generate snapshot from trajectory and ptraj cannot > read in the extra section, all the snapshot generated will have the > residue numbering start from 1. > > Pls advise. > > Thanks and regards. > Colvin > > > > On Thu, Apr 26, 2012 at 10:21 AM, case <case.biomaps.rutgers.edu> wrote: >> On Thu, Apr 26, 2012, colvin wrote: >>> >>> 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? >> >> I'm guessing that the chamber prmtop file has a CTITLE rather than a TITLE >> command(?). If so, It's certainly worth modifying ambpdb.F90 to look >> for CTITLE rather than TITLE, and recompiling. Ambpdb only uses a small >> fraction of the information in the prmtop file, so may well be happy with such >> a change. >> >> ....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 Thu Apr 26 2012 - 06:00:03 PDT