Thanks Yun, Have a look at http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx so you may have tips of how to improve you check. One thing I recorded that makes diff is that amber input files have 6 decimals of precision and PDB/GRO only 3.
Not knowing exactly what you did, but it sounds that 0.05% (for total pot energy?) is OK. Alan On 15 September 2011 06:18, Yun Shi <yunsh...@gmail.com> wrote: > Hi Alan, > > For example, in the Glycam_06g.dat file, you can find: > ........ > OH-CG-CG-OS 1 -1.10 0.0 -1 > ........ > > So this dihedral parameter has a force constant of -1.10, and this is what > I mean by "GLYCAM force field assigns negative force constants to some > dihedrals". > > I did try the GMX45 approach, and using the conversion factor 4.184, I got > a difference of about 0.05%. I am not sure if this is caused not setting > step size in the sander minimization. > > Regards, > Yun > > > > > > > > Date: Tue, 13 Sep 2011 12:03:10 +0100 > From: Alan <alanwil...@gmail.com> > Subject: Re: [gmx-users] Re: amb2gmx.pl to convert GLYCAM topology > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <caeznbznq98pbhjdr1smpogdtz_pgfqsk40izlfpq7-nizyw...@mail.gmail.com > > > Content-Type: text/plain; charset="utf-8" > > > 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 <yunsh...@gmail.com> 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 gmx-users@gromacs.org >> > 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 gmx-users-requ...@gromacs.org. >> > 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 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110913/f9bc31d1/attachment-0001.html >> >> ------------------------------ >> >> Message: 5 >> Date: Tue, 13 Sep 2011 16:46:44 +0530 >> From: om prakash <ombioi...@gmail.com> >> Subject: [gmx-users] Unsubscribe me Please >> >> To: gmx-users@gromacs.org >> Message-ID: >> <CAM5rxXNDPYi_aEEd+7efAmZoPex8B4Um5FwgJKg6hfm= >> t9y...@mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Unsubscribe me Please >> -- >> Om Prakash Sharma >> Ph.D Scholar & DIT JRF >> Centre for Bioinformatics >> Pondicherry University >> Pondicherry-605014 >> -------------- next part -------------- > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > 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
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists