iulek wrote:
Hi!
I am a very beginner, trying to make some dynamics of a protein in a
water box, after doing some (web) tutorials. I googled first for this
(possibly simple) error, found one reference, but cannot see it,
possibly because the gromacs site is under changes.
I ran pdb2gmx and editconf. Then at genbox I get the error:
"
Processing topology
-------------------------------------------------------
Program genbox, VERSION 4.0.5
Source code file: futil.c, line: 330
File input/output error:
RecA_nat_b4em.top
-------------------------------------------------------
"
So is the topology in the current working directory?
-Justin
The command line is:
> genbox -cp ${MOL}_in_box.gro -cs -p ${MOL}_b4em.top -o
${MOL}_b4em.gro << eof > genbox.log
eof
with variable MOL set to RecA_nat
The file RecA_nat_b4em.gro is output without problems.
I am using gromacs 4.0.5 under openSuSE 11.1.
Thanks,
Jorge
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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