[gmx-users] problem in topology file of protein-lipid bilayer system for grompp

[Mark Abraham]

nitu sharma wrote:
> Dear Justin
> 
>                             I am doing simulation of membrane protein .I 
> follow your tutorial for that I think its perfect for that. But I am 
> getting problem in doing inflategro step, I alredy discuss this problem 
> with you but now I am starting everything fresh  I have completed upto 
> concatanation of protein with lipid bilayer after that for packing of 
> lipid around protein I  am using inflategro script from teleman website 
> . Problem came in second step of inflategro i.e for energy minimisation 
> for this I need topology file of "protein-lipid system".
> I am giving you information in detail i.e -
> for topology file I have made changes in topol.top file which I got from 
> pdb2gmx command in first step for protein processing ,the topol .top 
> file is like  this-
> File 'topol.top' was generated
> ;       By user: nitu (504)
> ;       On host: localhost.localdomain
> ;       At date: Thu Apr 16 23:20:48 2009
> ;
> ;       This is your topology file
> ;       Grunge ROck MAChoS
> ;
> ; Include forcefield parameters
> #include "ffG53a6.itp"
> 
> ; Include chain topologies
> #include "topol_A.itp"
> #include "topol_B.itp"
> 
> ; Include water topology
> #include "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 generic topology for ions
> #include "ions.itp"
> 
> [ system ]
> ; Name
> Grunge ROck MAChoS
> 
> [ molecules ]
> ; Compound        #mols
> Protein_A           1
> Protein_B           1
> **********
> And the change topology file is like this-
> 
> ; Include forcefield parameters
> #include "ffG53a6_lipid.itp"
> 
> ; Include chain topologies
> #include "topol_A.itp"
> #include "topol_B.itp"
> 
> #ifdef POSRES
> #include "posre_A.itp"
> #include "posre_B.itp"
> #endif

I think you've been told before that this is garbage. 
[position_restraints] directives are components of a [moleculetype], and 
so must come before the [moleculetype] of a subsequent molecule. Your 
use of the last four #include preprocessing commands violates this. You 
should make two #ifdef POSRES sections appropriately.

> ; Include DMPC chain topology
> #include "dmpc.itp"
> 
> 
> [ system ]
> ; Name
> Protein in DMPC bilayer
> 
> [ molecules ]
> ; Compound        #mols
> Protein_A           1
> Protein_B           1
> DMPC               128
> 
> but when I gave this topology file to grompp it shws error-
> no. of coordinates in coordinate file doesn,t mach the topology file .

OK, so do the arithmetic and see what the problem is.

> Can you suggest me something for making topology file for protein-lipid 
> bilayer system. Is there any other method for making topology file ,I 
> have read in mannual chapter 5 but there is also mentioned same method.
> If possible please help me becoz without solving this problem I can't 
> move for furthur processing .
> 
> * My gro file of protein shows 9902 atoms .
> As you ask in previous mail is .itp file have [ molecules ] section the 
> answer is the .itp file haven't molecules section it have [molecule type 
> ] section can it also create problem for topology file working.

So you have 9902 atoms in your coordinate file. How many atoms are in 
protein A, protein B and the 128 copies of DMPC *according to their 
[moleculetype] definitions*?

Mark