[gmx-users] Re: Problem with minimizing the energy of the solvated system
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 5 23:57:53 CEST 2012
On 7/5/12 5:51 PM, jonas87 wrote:
> Protein-water.pdb has the following line:
> CRYST1 75.324 75.324 75.324 60.00 60.00 90.00 P 1 1
> But after adding the NA/CL ions with genion the CRYST1 line is missing
> entirely from the output file protein-solvated.pdb
> Could this be because of the bug u mentioned?
Sounds about right.
> I'm using the latest version of gromacs, that means this bug was
Likely it was not fully fixed; I recall a change to editconf, but maybe genion
needs a look as well.
> So it is ok to always output to .gro instead of .pdb?
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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