[gmx-users] position restraints

[Shima Arasteh]

Believe me I add this line to mdp file as you wrote in KALP-15-DPPC.

"define        = -DPOSRES_LIPID "

Also added these to top file.
#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif 
 But I get again this error that the "This probably means that you have inserted topology section "position_restraints"
in a part belonging to a different molecule than you intended to."

Why this doesn't match?? I think POSITION RESTRAINING is making me crazy! :((
Would you please help me? 

Thanks for 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: Monday, March 25, 2013 8:52 PM
Subject: Re: [gmx-users] position restraints



On 3/25/13 12:06 PM, Shima Arasteh wrote:
> Hi,
>
> I want to use position restraints on P atom types of POPC, and on my protein inserted in POPC.
> The inserted protein has 2 chains.
>
> 1.
>
> I made index files for each chain and then restrained them by these commands:
> #make_ndx -f minim.gro -o protein_chain_A.ndx
> #genrestr -f minim.gro -o protein_chain_A_posre.itp -fc 100000 100000 100000 -n protein_chain_A.ndx
>
> #make_ndx -f minim.gro -o protein_chain_B.ndx
> #genrestr -f minim.gro -o protein_chain_B_posre.itp -fc 100000 100000 100000 -n protein_chain_B.ndx
>
> #make_ndx -f minim.gro -o lipid_posre.ndx
> #genrestr -f minim.gro -o lipid_posre.itp -fc 100000 100000 100000 -n lipid_posre.ndx
>
> 2.
>
> Then these lines added to top of the itp files:
> #ifdef POSRE
> #endif
>
> 3.
> Then restrained them as follow in top file:
>
> ; 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
>
> ; Include POPC chain topology
> #include "popc.itp"
> #ifdef POSRE_LIPID
> #include "lipid_posre.itp"
> #endif
>
> 4.
>
> Also added the define statement to mdp file :
>
> define        = -DPOSRES_LIPID -DPOSRES
>
> But when I run the grompp and get the per-processed top, only the chain_A is included in position restraint!
>
> Would you please give me suggestions? They would be appreciated.

Again, "POSRE" and "POSRES" are different.  -DPOSRES will not trigger the #ifdef 
POSRE block.

-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

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