[gmx-users] GROMOS96 and POPE

Ugur Akgun ugur_iowa at hotmail.com
Tue Feb 6 18:30:41 CET 2007

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...

[uakgun at frontend 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


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