[gmx-users] protein-SWCNT md simulation

[Atila Petrosian]

Dear gromacs users

I'd like to study the interaction between carbon nanotube and a protein.
I used amber03 parameters for both protein and cnt.

I have made cnt.top for the nanotube by g_x2top and pr.top for protein by
pdb2gmx.

I made adjustments to cnt.top to become cnt.itp file to be #included in
pr.top file.

My cnt.top file is as follows:


; Include forcefield parameters
#include "./cnt.ff/forcefield.itp"

[ moleculetype ]
; Name            nrexcl
cnt                 3

[ atoms ]
.
.
.
[ bonds ]
.
.
.
[ pairs ]
.
.
.
[ angles ]
.
.
.
[ dihedrals ]
.
.
.

[ system ]
; Name
cnt

[ molecules ]
; Compound        #mols
cnt                 1

For creation the cnt.itp from cnt.top file, I deleted

; Include forcefield parameters
#include "./cnt.ff/forcefield.itp"

*** and ***

[ system ]
; Name
cnt

[ molecules ]
; Compound        #mols
cnt                 1

-----------------------------------

Then I added

; Include forcefield parameters
#include "./cnt.ff/forcefield.itp"

to the pr.top file so that first lines of pr.top are as follows:

; Include forcefield parameters
#include "amber03.ff/forcefield.itp"
#include "./cnt.ff/forcefield.itp"


and the end of pr.top file is as follows:

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include cnt topology
#include "cnt.itp"

; Include water topology
#include "amber03.ff/tip3p.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 "amber03.ff/ions.itp"

[ system ]
; Name
Protein-cnt complex

[ molecules ]
; Compound        #mols
Protein             1
cnt                 1


When I use grompp grompp -f em.mdp -c pr_cnt.gro -p pr.top -o em.tpr,

grompp give me the following error message:


WARNING 1 [file forcefield.itp, line 1]:
  Too few gb parameters for type
********************************************

Couldn't find topology match for atomtype
Aborted



Is my manner true?

How to resolve this problem?

Any help will highly appreciated.