[gmx-users] Re: inflate gro

[Justin A. Lemkul]

Sweta Iyer wrote:
> Hi Justin,
> 
> Thanx for the suggestion. This is how my topology looks like with the
> strong position restraint included for the protein:
> 
> ; Include forcefield parameters
> #include "gromos53a6.ff/forcefield.itp"
> 
> ; Include chain topologies
> #include "complex6_Protein_chain_X.itp"
> #include "complex6_Protein_chain_Y.itp"
> 
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> 
> #ifdef STRONG_POSRES
> #include "strong_posre.itp"
> #endif
> 

The two preceding #ifdef statements are the problem.  To which protein 
[moleculetype] do these apply?  The way the topology is interpreted, the chain X 
moleculetype ends when the chain Y section begins, so the position restraints 
are only being applied to chain Y, which is probably the cause of the fatal 
error.  For an example, please refer to the Gromacs site, which provides an 
example of this principle:

http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

> ; Include chain topology for DMPC
> #include "dmpc.itp"
> 
> ; Include water topology
> #include "gromos53a6.ff/spc.itp"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
> 
> ; Include topology for ions
> #include "gromos53a6.ff/ions.itp"
> 
> 
> [ system ]
> ; Name
> Protein
> 
> [ molecules ]
> ; Compound        #mols
> Protein_chain_X     1
> Protein_chain_Y     1
> DMPC		    125
> 
> I think the tutorial asks to include a section in the topology similar to
> this?!
> 
> 

Yes, but the issue is more complex when dealing with two proteins.  Knowing this 
up front would have probably saved some time.

-Justin

> 
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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