Asmaa Elsheshiny wrote:
Hi, all
when I want to use gromacs preprocessor grompp to obtain .tpr to use in the
energy minimization as follow
grompp -f minim.mdp -c bradywaterbox.gro -p brady.top -o minimbrady.tpr
I got the following error message
Fatal error:
number of coordinates in coordinate file (bradywaterbox.gro, 670)
does not match topology (brady.top, 0)
where, bradywaterbox.gro & brady.top are obtained from
genbox -cp solvatedbrady.gro -cs spc216.gro -o bradywaterbox.gro -p brady.top
I think that the topology file didnot include the solvent molecules so it
canont be mached with the coordinate file .gro , did it?
So how can I fix this problem?
There is a section regarding this error here:
http://www.gromacs.org/Documentation/Errors
grompp doesn't seem to think your topology has anything in it at all, so it's
not simply an issue of the waters.
-Justin
Regards,
Asmaa
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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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