[gmx-users] Re: inflate gro
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 21 05:35:27 CEST 2011
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"
> #ifdef STRONG_POSRES
> #include "strong_posre.itp"
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:
> ; 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
> ; Include topology for ions
> #include "gromos53a6.ff/ions.itp"
> [ system ]
> ; Name
> [ 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
Yes, but the issue is more complex when dealing with two proteins. Knowing this
up front would have probably saved some time.
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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