Dear all, Dear Justin,We have been working on setting up an MD experiment in which our system is made of three separate domains of a protein embedded in a DMPC bilayer surrounded by water.
We have generated a PDB file in which our three domains are labeled as A, B and C (in the column corresponding to the chain identifiers). Our system is labeled "mod", Chain A has 342 atoms, Chain B has 289 atoms and Chain C has 715 atoms. Somehow these identifiers are lost when we use pdb2gmx.
We have gone as far as Step Three of Justin's tutorial. It is here were we have encountered a problem.
The steps we have performed previously without trouble are: $ cat mod_newbox.gro dmpc_whole.gro > system.gro$ genrestr -f mod_newbox.gro -o strong_posre.itp -fc 100000 100000 100000 $ perl inflategro.pl system.gro 4 DMPC 14 system_inflated.gro 5 area.dat
When we wish to perform a minimization of the system via$ grompp -f minim_inflo.mpd -c system_inflated.gro -p topol_inflo.top -o em_system_inflated.tpr
the following error appears: ------------------------------------------------------- Program grompp_d, VERSION 4.5.3 Source code file: toppush.c, line: 1526 Fatal error: [ file strong_posre.itp, line 720 ]: Atom index (716) in position_restraints out of bounds (1-715).This probably means that you have inserted topology section "position_restraints"
in a part belonging to a different molecule than you intended to. In that case move the "position_restraints" section to the right molecule. ------------------------------------------------------- The topol_inflo.top file contains the following instructions: ------------------------------------------------------ ; Include forcefield parameters #include "gromos53a6_lipid.ff/forcefield.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #ifdef POSRES #include "posre_Protein_chain_A.itp" #endif #include "topol_Protein_chain_B.itp" #ifdef POSRES #include "posre_Protein_chain_B.itp" #endif #include "topol_Protein_chain_C.itp" #ifdef POSRES #include "posre_Protein_chain_C.itp" #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include "strong_posre.itp" #endif ; Include DMPC chain topology #include "dmpc.itp" ; Include water topology #include "gromos53a6_lipid.ff/spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "gromos53a6_lipid.ff/ions.itp" [ system ] ; Name mod.pdb [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 Protein_chain_C 1 DMPC 128 -------------------------------------------------- QUESTIONS 1) Do you see any problem in the topol_inflo.top setup? 2) Do we need to create a strong_posre.itp for each chain? Looking forward to hear your comments... Cheers, Ramon Garduno
<<attachment: ramon.vcf>>
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