[gmx-users] position restraint

[Mark Abraham]

"It doesn't work" is not enough information to lead anyone to a solution :-)

Mark

On Thu, Aug 22, 2013 at 6:53 PM, Shima Arasteh
<shima_arasteh2001 at yahoo.com> wrote:
> If you mean that I need to modify the posre_ion.itp file to:
>
>  ; position restraints for a_85563 of system
>
>  [ position_restraints ]
>  ;  i funct       fcx        fcy        fcz
> 1   1     100000     100000     100000
>
> It doesnt work.......... :-(
>
>
> Sincerely,
> Shima
>
>
> ----- Original Message -----
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>
> Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Thursday, August 22, 2013 6:37 PM
> Subject: Re: [gmx-users] position restraint
>
> 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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>>
>