Do you mean that I can just use the new version of pdb2gmx than change the included forcefield and in case the name of the atoms and it should work?
2012/2/16 Justin A. Lemkul <jalem...@vt.edu>: > > > francesca vitalini wrote: >> >> Hi all! >> I'm trying to create a topology file from the pdb using the pdb2gmx >> command of gromacs 3.3.1 but I'm encountering some issues. I should >> use the flag -tar in order to select interactively the termini, but >> with the old version of gromacs this is not implemented and I cannot >> use a new one because I need the reverse transformation tool which is >> only implemented in that version. > > > The topology format is largely unaffected by differences in version. A few > moments with a text editor to fix the #include statements written by a > version in the 4.5.x series would solve any problems. > > >> Here it is the pdb I'm using >> >> REMARK >> ATOM 1 1HH3 ACE 1 -3.547 1.520 1.054 >> ATOM 2 CH3 ACE 1 -3.081 0.536 0.999 >> ATOM 3 2HH3 ACE 1 -3.437 0.016 0.110 >> ATOM 4 3HH3 ACE 1 -3.348 -0.041 1.883 >> ATOM 5 C ACE 1 -1.570 0.683 0.929 >> ATOM 6 O ACE 1 -1.051 1.800 0.938 >> ATOM 7 N ALA 2 -0.862 -0.446 0.851 >> ATOM 8 H ALA 2 -1.368 -1.322 0.859 >> ATOM 9 CA ALA 2 0.607 -0.509 0.828 >> ATOM 10 HA ALA 2 0.997 0.272 1.484 >> ATOM 11 CB ALA 2 1.025 -1.867 1.412 >> ATOM 12 1HB ALA 2 2.113 -1.918 1.485 >> ATOM 13 2HB ALA 2 0.676 -2.677 0.770 >> ATOM 14 3HB ALA 2 0.604 -1.990 2.411 >> ATOM 15 C ALA 2 1.238 -0.262 -0.565 >> ATOM 16 O ALA 2 2.465 -0.181 -0.678 >> ATOM 17 N NAC 3 0.423 -0.139 -1.620 >> ATOM 18 H NAC 3 -0.569 -0.212 -1.447 >> ATOM 19 CH3 NAC 3 0.860 0.098 -2.992 >> ATOM 20 1HH3 NAC 3 1.413 1.037 -3.050 >> ATOM 21 2HH3 NAC 3 1.506 -0.718 -3.323 >> ATOM 22 3HH3 NAC 3 -0.006 0.155 -3.652 >> TER >> END >> >> >> And this is the pdb2gmx command >> path/pdb2gmx -ignh -missing -f struct1-1.pdb -p ala.top -o ala.gro >> >> >> I use the gromos9653a6 forcefield and the spc water model >> >> And this is the error I get >> >> There are 2 donors and 2 acceptors >> There are 2 hydrogen bonds >> ------------------------------------------------------- >> Program pdb2gmx, VERSION 3.3.1 >> Source code file: pdb2gmx.c, line: 383 >> >> Fatal error: >> Atom CH3 in residue ACE 1 not found in rtp entry with 3 atoms >> while sorting atoms >> ------------------------------------------------------- >> >> Any suggestions? > > > Check the .rtp file - your atom is named in a way that is inconsistent with > what the force field expects. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 -- Francesca Vitalini PhD student at Computational Molecular Biology Group, Department of Mathematics and Informatics, FU-Berlin Arnimallee 6 14195 Berlin vital...@zedat.fu-berlin.de francesca.vital...@fu-berlin.de +49 3083875776 +49 3083875412 -- 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