[gmx-users] position restraints

[Justin A. Lemkul]

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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