[gmx-users] position restraint

[Shima Arasteh]

So I made a specific ces.itp file, and made a separate section in top file :
ces.itp file:
[ moleculetype ]
; molname    nrexcl
Ces        1

[ atoms ]
; id    at type        res nr     residu name    at name  cg nr    charge   
1    CES        1    Ces        Ces     1    1         


.top  file:
; Include topology for ces
#include "ces.itp"
#ifdef POSRES_ION
#include "posre_ion.itp"
#endif
; Include topology for ions
#include "./charmm36-modified.ff/ions.itp"


The posre_ion.itp file contains:

; position restraints for a_85563 of system

[ position_restraints ]
;  i funct       fcx        fcy        fcz
85563   1     100000     100000     100000

But it doesnt work, would you please let me know if I had a mistake?

Thanks for your suggestions in earlier messages.


 
Sincerely,
Shima


----- Original Message -----
From: Mark Abraham <mark.j.abraham at gmail.com>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Thursday, August 22, 2013 5:54 PM
Subject: Re: [gmx-users] position restraint

Have a look at that file. It defines the [moleculetype] for lots of
ions, but you need a position restraint that applies to whichever
[moleculetype] is the one you want to use. That means it has to come
before the next [moleculetype]. As manual 5.7 says, the .top format is
hierarchical. So you need to modify the ions.itp, or make one that has
only the ion of interest.

Mark

On Thu, Aug 22, 2013 at 3:01 PM, Shima Arasteh
<shima_arasteh2001 at yahoo.com> wrote:
> Yes,
> But the part in which the ions are introduced is #include "./charmm36-modified.ff/ions.itp" ,
> Is this not the right place to write the posre_ion lines? As I see it is in agreement with  "Atom index n in position_restraints out of bounds" link.
> So what would be the solution? I don't see any itp file generated by pdb2gmx, for the ions such as chain A  and other moleculetypes ?
>
> Would you give me a hint and help me with it please?
>
> Sincerely,
> Shima
>
>
>
> ---------- Forwarded message ----------
> From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
> Date: Thu, 22 Aug 2013 03:54:07 -0700 (PDT)
> Subject: [gmx-users] position restraint
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
> Hi,
>
> I want to put position restraint on an ion ,
>
> First made an .itp file of the ion: posre_ion.itp
>
> Then added these line to top file:
> #include "./charmm36-modified.ff/ions.itp"
> #ifdef POSRES_ION
> #include "ion_posre.itp"
> #endif
>
> And added the line to mdp file
>
> define         = -DPOSRES_ION
>
> But the grompp failed because it gives me the fatal error that the
> include line is not in the correct position.
>
>
>
> Would you please let me know if the inclusion of posre_ion.itp is not
> as I did? What's the problem?
>
> Thanks in advance for your suggesions.
>
> 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
>
> --
> 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