[gmx-users] position restraints

[Shima Arasteh]

No, You have not shouted at me, never! But sometimes I think that I deserve to be shouted !!
I deeply appreciate your patience and attention. Thanks for your time and your replies. 

In my protein, chains A and B are identical. 



 
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: Tuesday, March 26, 2013 4:16 PM
Subject: Re: [gmx-users] position restraints



On 3/26/13 7:01 AM, Shima Arasteh wrote:
> 
> Hi Dear Justin
> 
> 
> First of all, I request you that not to shout at me! I am so sorry to ask you questions about position restraints again!
> 

I haven't done any shouting, but statements like this seem to imply that I have.  The point of this forum is post your questions, so if things still aren't clear, then you're welcome to post them.  Hopefully I have never given anyone the impression of anger or castigation in my answers.  Sometimes I am terse, but that's because I'm busy with my own work, and a short answer is preferable to a long one.

> I
>   know I have sent you such emails before, and you suggested me to read
> include file mechanism in web site. I did this and also read some emails
>   in forum. But I think I have problems with include mechanism. Again I
> got into the trouble about position restraining:
> 
> As you told me -DPOSRES will not trigger #ifdef POSRE or #ifdef DPOSRES.
> 
> I
>   have a system of POPC/ions/waters and a double chain protein inserted
> in POPC bilayer. I put restraints on P headgroups and protein. I added
> the define line to the mdp file as follow:
> define        = -DPOSRES_LIPID -DPOSRES
> 
> Then added the itp files to my top as follow:
> 
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #ifdef POSRE
> #include "protein_chain_A_posre.itp"
> #endif
> #include "topol_Protein_chain_B.itp"
> #ifdef POSRE
> #include "protein_chain_B_posre.itp"
> #endif
> 

#ifdef POSRE requires -DPOSRE, not -DPOSRES as you have above.  I've now said that three times (and you said it above!), so please be mindful of the advice you've been given and take care in what you're doing.

> ; Include POPC chain topology
> #include "popc.itp"
> #ifdef POSRES_LIPID
> #include "lipid_posre.itp"
> #endif
> 
> 
> But when I run the grompp with -pp flag, I see that restraints on chain_B are not included!
> 

I don't see how that's possible.  Position restraints for both chains are under the control of the same #ifdef condition, as shown above.  One cannot be restrained without the other.

> Then
>   I changed the numbering in protein_chain_B_posre.itp to what they are
> in their original itp file, generated earlier by pdb2gmx. Do you agree
> that it is the problem which I encountered with?

pdb2gmx should have provided you with suitable restraint .itp files when you produced the original topology, and will have written suitable #ifdef blocks to properly use them.  Have you manipulated these files in some way?  If you have, start over.  Use the files that pdb2gmx gave you until you can convince yourself that you know how to use them correctly, then apply whatever custom restraints you feel are necessary.  Learn to walk before you run.

> Now when I run grompp I see the restraints after each chains with the same numbering.
> 

I don't exactly know what this means.  Are chains A and B identical?  If they are, then this makes sense.

-Justin

-- ========================================

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

========================================