Hi Yun, Have you read http://ambermd.org/formats.html?
In particular, this note: """ NOTE: *the atom numbers in the following arrays that describe bonds, angles, and dihedrals are coordinate array indexes for runtime speed. The true atom number equals the absolute value of the number divided by three, plus one. In the case of the dihedrals, if the fourth atom is negative, this implies that the dihedral is an improper. If the third atom is negative, this implies that the end group interations are to be ignored. End group interactions are ignored, for example, in dihedrals of various ring systems (to prevent double counting of 1-4 interactions) and in multiterm dihedrals. * """ I may be failing to understand what you mean by "GLYCAM force field assigns negative force constants to some dihedrals". Anyway, since GMX 4.5 can go without RB convertions, you can do this: acpype -x disac.inpcrd -p disac.prmtop --gmx45 If you have sander, you can do just one step of EM and compare against one step EM with GMX. Do the proper conversions and Energies diff should be < 0.001%. Cheers, Alan On 12 September 2011 21:21, Yun Shi <[email protected]> wrote: > Hi all, > > I am not a CS person, but I did find something in acpype.py as > > ............. > if phase in [0, 180]: > properDihedralsGmx45.append([item[0].atoms, phaseRaw, > kPhi, period]) > if not self.gmx45: > if kPhi > 0: V[period] = 2 * kPhi * cal > if period == 1: > C[0] += 0.5 * V[period] > if phase == 0: > C[1] -= 0.5 * V[period] > else: > C[1] += 0.5 * V[period] > elif period == 2: > ...................... > > kPhi here seems to be the dihedral force constant, and it seems if kPhi < > 0, no value will be assigned to C[0], C[1], C[2] ... > > I wonder if the negative dihedral force constants problem could be solved > by changing 'kPhi > 0' to 'kPhi != 0' for acpype? > > Thanks, > > Yun > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588
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