Hi, On Friday 20 October 2006 03:30, Stefan Schöbel wrote: > I am using only a protein and the GROMOS96 43a1 force field. > After pdb2gmx I got: > Back Off! I just backed up test.top to ./#test.top.3# > Processing chain 1 (1594 atoms, 214 residues) > There are 288 donors and 315 acceptors > There are 479 hydrogen bonds > Will use HISB for residue 45 > Will use HISB for residue 79 > Will use HISB for residue 177 > Will use HISB for residue 202 > Checking for duplicate atoms.... > Now there are 1593 atoms. Deleted 1 duplicates. > Opening library file /home/mpaetzel/programs/share/gromacs/top/specbond.dat > 5 out of 5 lines of specbond.dat converted succesfully > Special Atom Distance matrix: > CYS102 > SG760 > CYS167 SG1251 2.930 > N-terminus: NH3+ > C-terminus: COO- > Now there are 214 residues with 1957 atoms > Making bonds... > Opening library file > /home/mpaetzel/programs/share/gromacs/top/aminoacids.dat Number of bonds > was 1996, now 1991 > Generating angles, dihedrals and pairs... > Before cleaning: 3360 pairs > Before cleaning: 3782 dihedrals > There are 1101 dihedrals, 946 impropers, 2896 angles > 3360 pairs, 1991 bonds and 0 virtual sites > Total mass 22620.601 a.m.u. > Total charge -18.000 e > Writing topology > > > --> why are the HIS residues changed into HISB?
you can change this interactivly with pdb2gmx. Option is -his (and others) > > after editconf: > > Generated 279 of the 1225 non-bonded parameter combinations > Excluding 3 bonded neighbours for Protein 1 > Excluding 2 bonded neighbours for SOL 7683 > Excluding 2 bonded neighbours for SOL 2730 > NOTE: > System has non-zero total charge: -1.800000e+01 > > > I tried adding C term Oxygen with spdbv as well, but it still the same > uneven charge. > > What happened? > > thanks in advance > > Stefan Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
