On 2012-03-12 22:56, saly jackson wrote:
Hi everybody
I want to build a simulation box fill of water and some SDS molecules.
To do this at first I fill the box with SDS molecules without their Na+
ions. Then I filled the simulation box with water molecules. After that,
I want to replace some water molecules with Na+ ions. I ran the
following commands:
genbox -ci SDS.pdb -nmol 10 -box 2 2 1.9 -p topol.top -o SDS-box.gro
genbox -cp SDS-box.gro -cs spc216.gro -p topol.top -o SDSWater.gro
grompp -f ions.mdp -c SDSWater.gro -p topol.top -o ions.tpr
But to run the last command I receive the following error:
you managed to cut the essential information before this, that would
help you to fix the problem yourself.
Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
"I managed to get two hours of work done before work" (E. Lindahl)
Would you please help me,
Thanks
Saly
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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