[gmx-users] Re: protein in SDS/water

[Justin A. Lemkul]

Anna Marabotti wrote:

<snip>

> [ moleculetype ]
> ; Name	nrexcl
> SDS	3
> 
> ; Include topology for SDS
> #include "SDS.itp"
> 

Isn't this moleculetype already specified within SDS.itp?  Perhaps posting the 
contents of SDS.itp will help solve this issue; the rest of the topology seems 
fine, except this section.

> [ system ]
> ; Name
> Protein in water with SDS
> 
> [ molecules ]
> ; Compound        #mols
> Protein             1
> SOL             36173
> SDS	        2000
> 

The [ molecules ] section must be in the same order as your coordinate file.

-Justin

> I hope 
> 
> ______________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science, CNR
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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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