[gmx-users] Problems with a three domain protein in a membrane

[Justin A. Lemkul]

Dr. Ramón Garduño-Juárez wrote:
> 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.
> 

Chain identifiers are not necessary for Gromacs programs to function.  If you 
wish to keep them, use .pdb format as the output of pdb2gmx rather than .gro, 
which does not contain this information.

> 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?
> 

No.

> 2) Do we need to create a strong_posre.itp for each chain?
> 

Yes.

http://www.gromacs.org/Documentation/How-tos/Position_Restraints

http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds

-Justin

> Looking forward to hear your comments...
> 
> Cheers,
> Ramon Garduno
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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