Hi Justin, Just to let you know that after reinstalling everything again with Fink it worked fine. I have no idea I hade such a problem.
Alan On Mon, Jun 15, 2009 at 23:05, Alan<alanwil...@gmail.com> wrote: > Hi Justin, > > Please, confirm this, you mean that this pdb worked for you with '-ignh'? > > Gosh... > > So I may not loosing my mind when I said that it was working before. > > So, I am running: > - Mac Osx 10.5.7 intel. > - Gromacs 4.0.5 (from Fink) with ffamber; > - Compilers from Fink. > > I ran test suite and although I got some fails for complex and > kernel, nothing for simple or pdb2gmx.? Anyway, I doubt tested suite > would fail because oplsaa is working fine here if I do 'pdb2gmx -f > GGG.pdb -ff oplsaa -ignh' > > In any case, many thanks for your attention Justin, > > Alan > > On Mon, Jun 15, 2009 at 20:01, <gmx-users-requ...@gromacs.org> wrote: >> Alan wrote: >>> Thank you Justin, >>> >>> You noticed well that. But this example was built to work without >>> -ignh and to exemplify my problem, because in real case I have this >>> protein and either I can use 'sed' to fix it (mainly H names) I found >>> it annoying sometimes, so why not -ignh? >>> >> >> No idea. I can successfully process your .pdb file with and without -ignh, >> and >> I get the same result (a correct topology) each time. Have you run the test >> suite to validate your installation? Maybe if you post the details of your >> hardware, compilers, OS, etc. someone can spot something that might be >> problematic (i.e., a bug). >> >> -Justin >> >>> Cheers, >>> Alan >>> >>> On Mon, Jun 15, 2009 at 15:51, <gmx-users-requ...@gromacs.org> wrote: >>> >>>> Alan wrote: >>>>> Hi there, >>>>> I am trying to understand why when doing: >>>>> >>>>> pdb2gmx -f GGG.pdb -ff amber99sb -ignh >>>>> >>>>> I am getting: >>>>> >>>>> WARNING: atom H is missing in residue GLY 2 in the pdb file >>>>> You might need to add atom H to the hydrogen database of residue >>>>> GLY >>>>> in the file ff???.hdb (see the manual) >>>>> >>>> I don't know why this is failing, but from the looks of your .pdb file, >>>> you have >>>> all the atoms you need, properly named and everything. Why do you need >>>> -ignh? >>>> >>>> -Justin >>>> >>>>> ------------------------------------------------------- >>>>> Program pdb2gmx, VERSION 4.0.5 >>>>> Source code file: pdb2top.c, line: 704 >>>>> Fatal error: >>>>> There were 1 missing atoms in molecule Protein_G, if you want to use >>>>> this incomplete topology anyhow, use the option -missing >>>>> ------------------------------------------------------- >>>>> >>>>> in /sw/share/gromacs/top/ffamber99sb.hdb I have: >>>>> >>>>> GLY 2 >>>>> 1 1 H N -C CA >>>>> 2 6 HA CA N C >>>>> >>>>> And I see nothing wrong with that. >>>>> >>>>> in /sw/share/gromacs/top/ffamber99sb.rtp: >>>>> >>>>> [ GLY ] >>>>> [ atoms ] >>>>> N amber99_34 -0.41570 1 >>>>> H amber99_17 0.27190 2 >>>>> CA amber99_11 -0.02520 3 >>>>> HA1 amber99_19 0.06980 4 >>>>> HA2 amber99_19 0.06980 5 >>>>> C amber99_2 0.59730 6 >>>>> O amber99_41 -0.56790 7 >>>>> >>>>> Which is pretty OK too. >>>>> >>>>> Besides, I don't get any error for NGLY or CGLY. Only "atom H is >>>>> missing in residue GLY 2". If I mess with ffamber99sb.hdb for GLY I >>>>> got others messages stating the other missing atoms. >>>>> OPLS, which is very similar, works fine. >>>>> >>>>> The pdb is as simple as this: >>>>> ATOM 1 N NGLYG 1 59.012 0.129 -0.254 1.00 0.00 >>>>> ATOM 2 H1 NGLYG 1 58.484 0.488 0.618 1.00 0.00 >>>>> ATOM 3 H2 NGLYG 1 58.683 0.775 -1.007 1.00 0.00 >>>>> ATOM 4 H3 NGLYG 1 58.789 -0.895 -0.326 1.00 0.00 >>>>> ATOM 5 CA NGLYG 1 60.467 0.239 -0.366 1.00 0.00 >>>>> ATOM 6 HA1 NGLYG 1 60.728 1.248 -0.251 1.00 0.00 >>>>> ATOM 7 HA2 NGLYG 1 60.773 -0.150 -1.355 1.00 0.00 >>>>> ATOM 8 C NGLYG 1 61.175 -0.584 0.690 1.00 0.00 >>>>> ATOM 9 O NGLYG 1 60.636 -0.753 1.809 1.00 0.00 >>>>> ATOM 10 N GLY G 2 62.471 -1.163 0.322 1.00 0.00 >>>>> ATOM 11 H GLY G 2 62.882 -1.173 -0.678 1.00 0.00 >>>>> ATOM 12 CA GLY G 2 63.150 -1.717 1.498 1.00 0.00 >>>>> ATOM 13 HA1 GLY G 2 62.745 -2.672 1.656 1.00 0.00 >>>>> ATOM 14 HA2 GLY G 2 63.047 -1.068 2.389 1.00 0.00 >>>>> ATOM 15 C GLY G 2 64.648 -1.799 1.285 1.00 0.00 >>>>> ATOM 16 O GLY G 2 65.151 -2.016 0.165 1.00 0.00 >>>>> ATOM 17 N CGLYG 3 65.503 -1.595 2.460 1.00 0.00 >>>>> ATOM 18 H CGLYG 3 65.152 -1.325 3.447 1.00 0.00 >>>>> ATOM 19 CA CGLYG 3 66.902 -1.817 2.091 1.00 0.00 >>>>> ATOM 20 HA1 CGLYG 3 67.178 -1.043 1.438 1.00 0.00 >>>>> ATOM 21 HA2 CGLYG 3 67.022 -2.819 1.632 1.00 0.00 >>>>> ATOM 22 C CGLYG 3 67.808 -1.809 3.299 1.00 0.00 >>>>> ATOM 23 OC1 CGLYG 3 67.222 -1.605 4.509 1.00 0.00 >>>>> ATOM 24 OC2 CGLYG 3 69.135 -2.006 3.077 1.00 0.00 >>>>> >>>>> >>>>> My memory may fail, but I can swear it was working before... >>>>> >>>>> Many thanks in advance, >>>>> Alan >>> >> > > -- > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate > Department of Biochemistry, University of Cambridge. > 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>>http://www.bio.cam.ac.uk/~awd28<< > -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< _______________________________________________ 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/search before posting! 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