[gmx-users] Strong position restrain

[Peter C. Lai]

Postion restraints for a given topology must appear in the same section as
the current molecule's toplogy before the next new [molecule_type].

So you need to #include position_restraints.itp after the topol.itp.:

 #include "topol_Protein_A.itp"
 #ifdef POSRE
 #include "strong_posre.itp"
 #endif
 #include "topol_Protein_B.itp"
 #ifdef POSRE
 #include "strong_posre.itp"
 #endif

On 2012-09-22 02:39:58AM -0700, Shima Arasteh wrote:
> Dears,
> 
> As explained it many times before, I am simulating a system of water, dimer protein and water. I am doing this simulation by getting idea from KALP15-DPPC tutorial. 
> 
> First of all, when I get the top file, I don't see the section of position restrains in top file. My generated top file is as below:
> 
> ; Include forcefield parameters
> #include "./charmm36-modified.ff/forcefield.itp"
> 
> ; Include chain topologies
> #include "topol_Protein_A.itp"
> #include "topol_Protein_B.itp"
> 
> ; Include POPC chain topology
> #include "popc.itp"
> 
> ; Include water topology
> #include "./charmm36-modified.ff/tip3p.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 "./charmm36-modified.ff/ions.itp"
> 
> [ system ]
> ; Name
> Gromacs Runs One Microsecond At Cannonball Speeds
> 
> [ molecules ]
> ; Compound        #mols
> Protein_A            1
> Protein_B            1
> 
> 1. I'd like to know why? Is it not expected?
> 
> Secondly, to put a strong position restrain on protein, I added the "Strong position restraints for InflateGRO" after FF section. grompp gives me an error of invalid order:
> Fatal error:
> Syntax error - File strong_posre.itp, line 3
> Last line read:
> '[ position_restraints ]'
> Invalid order for directive position_restraints
> 
> 
> 2. Would you please give me your suggestion? 
> 
> Thanks in advance.
> 
>  
> Sincerely,
> Shima
> -- 
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-- 
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Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
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