[gmx-users] position restraints

[Justin Lemkul]

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

-- 
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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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