[gmx-users] position restraint

[Mark Abraham]

Now you have a [moleculetype] with one atom and hopefully a position
restraint. But its [position_restraints] wants to act on atom 85563 of
the molecule, which does not exist! See newly updated
http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

Mark

On Thu, Aug 22, 2013 at 3:58 PM, Shima Arasteh
<shima_arasteh2001 at yahoo.com> wrote:
> 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
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>