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

[Justin Lemkul]

On 3/18/13 3:05 AM, Shima Arasteh wrote:
> 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?
>

Clearly.  Fatal errors mean something is very wrong.  In principle, what you 
showed before was correct.  If that wasn't an actual topology snippet or you've 
done something else wrong, then I haven't seen what it is.

-Justin

> 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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