[gmx-users] error in pdb2gmx

Dmitriy Golubobsky dmitriy.golubovsky at gmail.com
Thu Dec 7 23:55:35 CET 2006

Please, give an adive.

I've add new residues to ffoplsaa.rtp
build pdb file.
and try to convert it to gromacs format.
under WindowsXP, using GROMACS 3.2.1 everyting is OK.
but, when i did the same comman under GROMACS 3.3.1 (SuSE),
i've got an error:

Read 4904 atoms
Opening library file /usr/local/gromacs/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 258 residues with 4904 atoms

  chain  #res #atoms
  1 ' '   258   4904

All occupancy fields zero. This is probably not an X-Ray structure
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp
Program pdb2gmx, VERSION 3.3.1
Source code file: resall.c, line: 289

Fatal error:
in .rtp file at line:


"These Gromacs Guys Really Rock" (P.J. Meulenhoff)

What I'm doing wrong?
Dmitriy Golubovsky
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