Dmitriy Golubobsky wrote:
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?
This is only a guess, but if your .rtp file uses Windows line-endings
and pdb2gmx is sensitive to that, you might see such a problem. Use
dos2unix on all your ex-Windows files and see how you go.
Mark
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