Hi Urgur, as I said: you DON'T HAVE to suck the POPE through pdb2gmx - with the files provided, you can DIRECTLY start your calculations! Bye Steffen > Hi Steffen; > Thank yu very much for your email... > I did your recipe; > - edited the lipid info to ffG43a2bon.itp > - edited the lipid info to ffG43a2nb.itp > - put #include "pope.itp" into my *.top file > > I also edited lipid info to ffG43a2.rtp file (I didthis because the > file in the error resall.c checks the rtp file and says POPE not found > in database). > > but I still get the same error.. pasted below.... > > I'd appreciate any idea... > > thanks a lot... > > > [EMAIL PROTECTED] GROMACS]$ pdb2gmx -f try8.pdb -o try8.gro -ignh > > . > . > . > CYS1090 SG7989 1.580 > CYS1095 SG8018 2.149 1.146 > N-terminus: PRO-NH2+ > C-terminus: COO- > Now there are 1155 residues with 10692 atoms > Chain time... > > Back Off! I just backed up topol_A.itp to ./#topol_A.itp.6# > Making bonds... > Warning: Long Bond (3564-3566 = 6.97748 nm) > Warning: Long Bond (7127-7129 = 6.83609 nm) > Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat > Number of bonds was 10896, now 10892 > Generating angles, dihedrals and pairs... > Before cleaning: 17483 pairs > Before cleaning: 21269 dihedrals > There are 5426 dihedrals, 5837 impropers, 16017 angles > 17483 pairs, 10892 bonds and 0 virtual sites > Total mass 119933.121 a.m.u. > Total charge 6.000 e > Writing topology > > Back Off! I just backed up posre_A.itp to ./#posre_A.itp.7# > Processing chain 2 'B' (22246 atoms, 454 residues) > There are 454 donors and 0 acceptors > There are 0 hydrogen bonds > ------------------------------------------------------- > Program pdb2gmx, VERSION 3.3.1 > Source code file: resall.c, line: 438 > > Fatal error: > Residue 'POPE' not found in residue topology database > > ------------------------------------------------------- > > _________________________________________________________________ > Check out all that glitters with the MSN Entertainment Guide to the > Academy Awards® > http://movies.msn.com/movies/oscars2007/?icid=ncoscartagline2 > > _______________________________________________ > gmx-users mailing list [email protected] > 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
-- Dipl.-Chem. Steffen Wolf Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [EMAIL PROTECTED] Web: http://www.bph.rub.de _______________________________________________ gmx-users mailing list [email protected] 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
