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

[Justin A. Lemkul]

Justin A. Lemkul wrote:
> 
> 
> 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.
> 

Well, actually yes, but hopefully that was clear from the notes below.  I was 
thinking of the problem in terms of the arrangement of molecule names, etc.

Sorry for any confusion.

-Justin

>> 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
>>
>>
> 

-- 
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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

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