Yanmei Song wrote:
Dear Justin and Dallas:
Thank you for your help earlier.
I made a copy of ffoplsaa.rtp to my working directory and add a new
residue to it. Then perform the following command:
pdb2gmx -f pdms10.pdb -o pdms10.gro -p top.top -i pdms10.itp
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/FF.dat
Select the Force Field:
0: GROMOS96 43a1 force field
1: GROMOS96 43b1 vacuum force field
2: GROMOS96 43a2 force field (improved alkane dihedrals)
3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
7: Encad all-atom force field, using scaled-down vacuum charges
8: Encad all-atom force field, using full solvent charges
6
Opening library file ffoplsaa.rtp
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
Reading pdms10.pdb...
Read 45 atoms
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 45 atoms
chain #res #atoms
1 'A' 1 45
All occupancies are one
Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: resall.c, line: 289
Fatal error:
in .rtp file at line:
Well that's weird. You should use the "diff" utility on ffoplsaa.rtp
before and after your modifications and see what that tells you.
If you've edited it on a Windows machine, then you may have line-ending
issues. If so, use "dos2unix" on the file.
Mark
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