[gmx-users] CNT

[trevor brown]

Dear Justin,
Regarding our previous discussion under "CNT" topic, you want to know
exactly what I did to define C-C interaction. I have summarized it below.

1. I copied oplsaa.ff folder in my working directory
2. I added following lines to atomname2type.n2t
C    opls_995    0      12.011  2    C  0.142  C 0.142
C    opls_996    0      12.011  3    C  0.142  C 0.142  C 0.142
C    opls_997    0      12.011  4    C  0.142  C 0.142  C 0.142 C 0.142
C    opls_998    0      12.011  5    C  0.142  C 0.142  C 0.142 C 0.142 C
0.142
3. I added those to atomtypes.atp
 opls_995   12.01100  ;
 opls_996   12.01100  ;
 opls_997   12.01100  ;
 opls_998   12.01100  ;

4. I added those to ffbonded.itp
[ bondtypes ]
  C     C    1   0.14210   478900
 [ angletypes ]
  C   C    C  1 120.000 562.2
 [ dihedraltypes ]
5. I constructed .top file for CNT with the following, then I converted it
into .itp by vi editor
g_x2top -f cnt.gro -o cnt.top -nopairs -nexcl 5
6. By pdb2gmx, I obtained .top for peptide then I converted it into .itp
7. I combined CNT and peptide's pdbs in pymol and saved.
8. I wrote a .top file given below,
;
; File 'topol.top' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Mon Jan 10 02:51:19 2011
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.5.3
;
; Command line was:
; pdb2gmx -ignh -f vpgvg10.pdb
;
; Force field was read from the standard Gromacs share directory.
;
; Include forcefield parameters
#include "forcefield.itp"

; Include topology for CNT
#include "cnt.itp"
; Include topology for UW1
#include "uw1.itp"
; Include water topology
#include "spc.itp"
[ system ]
; Name
Protein and CNT in water
[ molecules ]
; Compound        #mols
Protein             1
CNT                 1
SOL                 4019
9. When I make grompp for minimization it givea me the following error
WARNING 1 [file ffbonded.itp, line 2703]:
  Overriding Bond parameters.
  old: 0.151 292880 0.151 292880
  new: C     C    1   0.14210   478900

ERROR 1 [file ffbonded.itp, line 2707]:
  Not enough parameters
Generated 334153 of the 334153 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 334153 of the 334153 1-4 parameter combinations
-------------------------------------------------------
Program grompp, VERSION 4.5.3
Source code file: toppush.c, line: 1166
Fatal error:
Atomtype opls_996 not found

That is all what I exactly did. Is anything wrong or missing?

best wishes
trevor
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