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

[Shima Arasteh]

Thanks for your replies.
As you suggested, I did as follows:
1. made index groups of two chains of my protein
2.Then applied genrestr in this command to generate 2 itp files: chainA_posre.itp and chainB_posre.itp 
#genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 100000 100000 100000 -n index-chain.ndx
#genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 100000 100000 100000 -n index-chain.ndx

3.Next, I included the itp files as follow in my top file:

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef DPOSRE
#include "chainA_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef DPOSRE
#include "chainB_posre.itp"
#endif

4. I also added this line to my mdp file:
define         = -DPOSRE

5. In addition I added these at the top of itp files for bothe restrained chains:
#ifdef DPOSRE
#endif

Now when I run the command :
grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr

I don't get any errors.
But when I run the mdrun I don't see any position restraint terms in my log file.
Would you please let me know your suggestions in this about? Did I do any steps by mistake?


Thanks in advance.
Sincerely,
Shima


________________________________
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, March 16, 2013 4:06 PM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints



On 3/16/13 8:34 AM, Shima Arasteh wrote:
> Thanks.
> As I understood from your emails, I need to make index groups of separate chains of my protein, use the index file in order to use in genrestr command and then include the specific itp files for each groups in top file?
> Do you mean this? Am I right?
> 

Yes.  Try it.

> One more thing that I need to know is that how it is possible to make an index group except the options appear after running make index command?
> 

Type 'help' at the prompt or otherwise search gromacs.org and Google for example usage.  It is very easy to create index groups specifying subsets of residues or just their backbone atoms, etc.

-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

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