[gmx-users] GROMOS96 and POPE

[Steffen Wolf]

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...
>
>
> [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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-- 
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: swolf at bph.rub.de
Web: http://www.bph.rub.de