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
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