[gmx-users] Strong position restrain

[Shima Arasteh]

 Oh, I really appreciate you Peter. I didn't know it at all!
:-) Thanks.


Sincerely,
Shima


----- Original Message -----
From: Peter C. Lai <pcl at uab.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Saturday, September 22, 2012 1:23 PM
Subject: Re: [gmx-users] Strong position restrain

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
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
==================================================================
Peter C. Lai            | University of Alabama-Birmingham
Programmer/Analyst        | KAUL 752A
Genetics, Div. of Research    | 705 South 20th Street
pcl at uab.edu            | Birmingham AL 35294-4461
(205) 690-0808            |
==================================================================