[gmx-users] position restraints
Justin A. Lemkul
jalemkul at vt.edu
Thu Jun 3 15:43:18 CEST 2010
abdullah ahmed wrote:
> Hi!
>
> In your previous mail you mentioned:
>
> The position restraints must belong to the [moleculetype] of
> the species to be restrained. * Once you #include a new molecule, you
> start a new
> [moleculetype] entry and the position restraints belong to it. *
>
>
> So I rechecked my .top file and found that [moleculetype] only occurs
> once. Perhaps I have misunderstood you. So I added the top file below. I
No it doesn't. Each time you #include a new .itp file, you are telling grompp
to copy and paste the contents of that .itp file in that location. Have a look
at spc.itp - it starts a new moleculetype.
http://www.gromacs.org/Documentation/Include_File_Mechanism
Note how the automatically-generated "posre.itp" file is #included at the end of
the Protein_A moleculetype, *before* any other molecules are introduced. You
have to do the same with any new #include statements or directives you add.
-Justin
> did not add the contents of [atoms] [bonds] etc because I felt the mail
> would become unnecessarily long.
>
> ; Include forcefield parameters
> #include "ffoplsaa.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> Protein_A 3
>
> [ atoms ]
>
> [ bonds ]
>
> [ pairs ]
>
> [ angles ]
>
> [ dihedrals ]
>
> [ dihedrals ]
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include water topology
> #include "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 generic topology for ions
> #include "ions.itp"
>
> [ system ]
> ; Name
> Protein
>
> [ molecules ]
> ; Compound #mols
> Protein_A 1
>
> Thanks again for your help,
> Abdullah
>
>
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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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