[gmx-users] no SOL in topology file after genbox command
Peter C. Lai
pcl at uab.edu
Fri Jun 29 12:15:18 CEST 2012
Make sure your top file #include ff/spc.itp
On 2012-06-29 11:35:24AM +0200, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi everybody,
> I wanted to add water in the box where I put the protein with the command
> genbox -cp 3m71_box.gro -cs spc216.gro -p 3m71.top -o 3m71_water.gro
> 2>>logErr 1>>logOut
> The result is that I have indeed water (SOL) in the protein file
> (3m71_water.gro). But there is a problem in the topology file (3m71.top).
> Here I only have the line in the end after [ molecules ] where it is
> written how many SOL were added to the structure:
> SOL 14329
> But in the [ moleculetype ] part of the topology file there is no SOL
> mentioned. This causes an error when I want to call grompp.
> SO my question is: why is there no SOL in the [ moleculetype ] part?
> Best, Eva
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Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
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