Fwd: [gmx-users] scripts to generate topology CG

[Justin A. Lemkul]

Francesco Pietra wrote:

>> grep W solvated.gro | wc -l
>>
>> and use that number in the topology?
> 
> I forgot to add that the graphic program uses the above grep command,

I don't understand this statement.

> giving the same number of W as the line command. The number of DCCP is
> diminished by those deleted in inserting the protein, but the grompp
> command complains that .gro does not matches .top. If no further water
> is added graphically, everything works.

This is where exact commands (in sequence) really help, or at least a stepwise 
procedure.  Are you adding a protein into a box that contains DCCP+water, or are 
you inserting the protein into DCCP, then adding water?

What is the exact error that grompp is giving you?  That the number of 
coordinates don't match? atom names don't match?

-Justin

-- 
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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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