On 4/15/13 6:58 AM, Ahmet yıldırım wrote:
I have the following files in directory
1.tip5p.gro
2.topol.top
3.em.mdp
topol.top:
#include "oplsaa.ff/forcefield.itp"
#include "oplsaa.ff/tip5p.itp"
[ system ]
water
[ molecules ]
SOL 512
commands:
editconf -f tip5p.gro -o protein-PBC.gro -bt cubic -d 1.0
genbox -cp protein-PBC.gro -cs tip5p.gro -p topol.top -o protein-water.gro
topol.top after genbox command:
#include "oplsaa.ff/forcefield.itp"
#include "oplsaa.ff/tip5p.itp"
[ system ]
water
[ molecules ]
grompp -v -f minim.mdp -c protein-water.gro -p topol.top -o
protein-water.tpr
Fatal error:
No molecules were defined in the system
There isnt the number of water molecules in topol.top after genbox command.
I dont understand why they have been deleted.
I cannot reproduce this problem with version 4.6, but it's trivial to just add
the correct number of water molecules in the topology by hand.
-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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