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
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