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

[Shima Arasteh]

Thanks for all your replies.
But I' d like to know what the meanings of S and D are? Why sometimes we should write DPOSRE, sometimes POSRE, and sometimes DPOSRES?



Sincerely,
Shima


________________________________
From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
To: Justin Lemkul <jalemkul at vt.edu>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, March 18, 2013 10:35 AM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints

To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I get the fatal error. This error states that I have inserted topology section "position_restraints" in a wrong place. I checked again the itp files included in my top file. They are matched correctly!  Did I modified the settings incorrectly? 

What would be other potent problems?

Please help me.
Thanks for your help.



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: Sunday, March 17, 2013 5:19 PM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints



On 3/17/13 6:50 AM, Shima Arasteh wrote:
> 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?
>

Yes, again there is a problem with the #ifdef statements.  If you use:

#ifdef DPOSRE
...
#endif

the corresponding "define" statement is -DDPOSRE.  Think of the first "D" in the 
"define" statement as "I am defining the following string to be true."  Your 
.mdp file corresponds to the use of:

#ifdef POSRE
...
#endif

-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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