On 1/8/13 1:37 AM, Payman Pirzadeh wrote:
Dear Justin,
Thanks for your suggestions. It all made sense.
But I ran into a strange problem. I checked the mail list, and all I found
was about misspelling the force field name. I copied the whole gromos53a5.ff
directory into my working folder, copied the modified .rtp, .dat and .hdb
files into the gromos53a5.ff folder, and issued:
pdb2gmx_d_mpi -f protein.pdb -p protein-CYA.top -o protein-CYA.gro -inter
-ff gromos53a5.ff
but what I got was:
Program pdb2gmx_d_mpi, VERSION 4.5.4
Source code file: pdb2top.c, line: 239
Fatal error:
Could not find force field 'gromos53a5.ff' in current directory, install
tree or GMXDATA path.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
If I do not add the -ff option, the default pdb2gmx command works, by
opening the force field from the default path. I tried 'source GMXRC' from
my working folder, but same error pops up. I am not sure what I am missing
here?!
You're using the wrong syntax. The option -ff should take just the prefix of
the force field directory, i.e. "-ff gromos53a5" which causes pdb2gmx to search
for a gromos53a5.ff directory.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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