[gmx-users] position restraints

[Shima Arasteh]

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.
Thanks in advance.


 
Sincerely,
Shima