Fwd: Fw: Fwd: [gmx-users] position restraints

[Shima Arasteh]

Do you mean that I need to make 2 backbone_posre.itp files for 2 chains?
It would not be possible because I don't see any option for seperate chains when running genrestr command.


Thanks in advance.

Sincerely,
Shima


________________________________
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> 
Sent: Saturday, March 16, 2013 2:21 PM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints





On Sat, Mar 16, 2013 at 9:40 AM, Shima Arasteh <shima_arasteh2001 at yahoo.com> wrote:

As you said I changed define in mdp file to define=-DPOSRE .
>
>I also included backbone.itp file as this:
>
>
>; Include chain topologies
>#include "topol_Protein_chain_A.itp"
>#ifdef POSRE
>#include "backbone_posre.itp"
>
>#endif
>#include "topol_Protein_chain_B.itp"
>#ifdef POSRE
>#include "backbone_posre.itp"
>#endif
>
>
> ; 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
>Protein
>
>[ molecules ]
>; Compound        #mols
>Protein_chain_A     1
>Protein_chain_B     1
>POPC        238
>SOL    19936
>CL    2
>
>But I get this fatal error that my include part for position restraints is not correct:
>Fatal error:
>[ file backbone_posre.itp, line 79 ]:
>Atom index (364) in position_restraints out of bounds (1-360).
>This probably means that you have inserted topology section "position_restraints"
>in a part belonging to a different molecule than you intended to.
>In that case move the "position_restraints" section to the right molecule.
>For more information and tips for troubleshooting, please check the GROMACS
>website at http://www.gromacs.org/Documentation/Errors
>
>Would you please give me suggestions?
>

The error message already did... Your chains are not identical. You are applying the same position restraints file to them. GROMACS doesn't know what you mean.

Mark


>Thanks in advance.
>
>Sincerely,
>Shima
>
>
>----- Original Message -----
>From: Justin Lemkul <jalemkul at vt.edu>
>To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
>Cc:
>Sent: Saturday, March 16, 2013 12:25 AM
>Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
>
>
>
>On 3/15/13 9:43 AM, Shima Arasteh wrote:
>> I also included the position restraints as follows in my top file:
>>
>> ; Include chain topologies
>> #include "topol_Protein_chain_A.itp"
>> #ifdef POSRE
>> #include "backbone_posre.itp"
>> #include "strong_posre.itp"
>> #endif
>> #include "topol_Protein_chain_B.itp"
>> #ifdef POSRE
>> #include "strong_posre.itp"
>> #include "backbone_posre.itp"
>> #endif
>>
>> As I described earlier, I included position restraints of backbone in top file and also added define = -DPOSRES to minim.mdp file. But it seems that the position restrains have not been included. Would you please suggest me how I can apply position restraints effectively?
>>
>
>It won't work because -DPOSRES doesn't trigger #ifdef POSRE.  To match your
>topology, what you need is -DPOSRE.  It is very easy to tell when position
>restraints are being applied.  A position restraint energy term is written to
>the .log and .edr files.  If it's not there, you're not applying restraints.
>
>-Justin
>
>> Thanks in advance.
>> Your suggestions would be appreciated.
>> Shima
>>
>>
>> ---------- Forwarded message ----------
>> From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
>> Date: Fri, 15 Mar 2013 05:50:09 -0700 (PDT)
>> Subject: Fw: Fwd: [gmx-users] position restraints
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>
>> Dear users,
>>
>>
>> Although I put the position restraints on backbone, I get RMSD around
>> 0.2 nm. Is it usual?
>> This deviation is just for a minimization step only. I' m on doubt
>> about keeping the backbone in a fix secondary structure.
>> I' d prefer to restraint the backbone completely. Is it possible?
>>
>> Thanks in advance.
>>
>>
>>
>> Restraints allow, by definition, for slight deviations.
>>
>> Erik
>> * Please don't post (un)subscribe requests to the list. Use thewww
>> interface or send it to gmx-users-request at gromacs.org.
>>
>>
>>
>>
>> Dear gmx users,
>>
>> I want to use restraints on backbone of my protein to keep its secondary
>> structure during minimization and equilibration steps. To do so, I
>> generated backbone-restrain.itp and then included it to top file. Next,
>> added define = -DPOSRES to minim.mdp file.
>> After minimization, when I check the minimization output file, I saw
>> that the backbone of input and output files are not exactly the same.
>> Is there any step which I have not done to set the restraints correctly?
>>
>>
>> Thanks in advance.
>>
>> Sincerely,
>> Shima
>>
>
>--
>========================================
>
>Justin A. Lemkul, Ph.D.
>Research Scientist
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>========================================
>
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