[gmx-users] grompp error for CNT+surfactant simulation

[niaz poorgholami]

Dear all
I am using Gromacs 4.5.3 to simulate a system including:
CNT+water+surfactant and I want to
use opls force field for my whole system.
so far I have done following things:
1.I copied oplsaa.ff folder in my working directory.
2.I added following lines to atomname2type.n2t
C    opls_995    0      12.011  1    C  0.142
C    opls_996    0      12.011  2    C  0.142  C 0.142
C    opls_997    0      12.011  3    C  0.142  C 0.142  C 0.142
C    opls_998    0      12.011  4    C  0.142  C 0.142  C 0.142 C 0.142
3.I added these to ffbonded.itp
[ bondtypes ]
 C   C  1   0.14210   478900

 [ angletypes ]
 C   C   C   1  120.000  397.480

[ dihedraltypes ]
 C   C   1   0.000 167.360  1
4.I added these to ffnonbonded.itp
opls_995   C      6    12.01100     0.000       A    3.851000e-01
4.39600e-01
 opls_996   C      6    12.01100     0.000       A    3.851000e-01
4.39600e-01
 opls_997   C      6    12.01100     0.000       A    3.851000e-01
4.39600e-01
 opls_998   C      6    12.01100     0.000       A    3.851000e-01
4.39600e-01
5.I used g_x2top to create topology for CNT.
Command line was:
g_x2top -f cnt.pdb -o cnt.top -r cnt.rtp -name CNT -nexcl 5

6.I used TopolGen to produce the *.itp file for surfactant molecule.
7.I placed surfactant molecules around CNT.
8.I used editconf using this command:
editconf -f cnt_sur.pdb -o cnt_sur.gro -c -d 1 -bt cubic
9. I wrote a  a .top file given below,
 Include forcefield parameters
#include "./oplsaa.ff/forcefield.itp"
; Include topology for DTAB
#include "DTAB.itp"
; Include topology for CNT
#include "cnt.itp"
;
[ molecules ]
; molecule name          nr.
DTAB                      14
CNT                       1

10.I called genbox with the command:
genbox -cp cnt_sur.gro -cs spc216.gro -p topol.top -o solv.gro
11.I added manually  these to topol.top
; Include SPC water topology
#include "oplsaa.ff/spc.itp"

12. once I run grompp : grompp -f em.mdp -c solv.gro -p topol.top -o
ions.tpr
I got following errors:
Ignoring obsolete mdp entry 'title'

WARNING 1 [file ffbonded.itp, line 2704]:
  Overriding Bond parameters.

  old: 0.151 292880 0.151 292880
  new: C   C  1   0.14210   478900

Generated 335790 of the 335790 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 335790 of the 335790 1-4 parameter combinations

ERROR 1 [file DTAB.itp, line 104]:
  No default Bond types


ERROR 2 [file DTAB.itp, line 105]:
  No default Bond types


ERROR 3 [file DTAB.itp, line 241]:
  No default Angle types


ERROR 4 [file DTAB.itp, line 242]:
  No default Angle types


ERROR 5 [file DTAB.itp, line 244]:
  No default Angle types


ERROR 6 [file DTAB.itp, line 245]:
  No default Angle types


ERROR 7 [file DTAB.itp, line 249]:
  No default Angle types


ERROR 8 [file DTAB.itp, line 302]:
  No default Ryckaert-Bell. types


ERROR 9 [file DTAB.itp, line 303]:
  No default Ryckaert-Bell. types

Excluding 3 bonded neighbours molecule type 'DTAB'
Excluding 5 bonded neighbours molecule type 'CNT'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file topol.top, line 27]:
  System has non-zero total charge: 5.039999e+00




There was 1 note

There was 1 warning

-------------------------------------------------------
Program grompp, VERSION 4.5.3
Source code file: /build/buildd/gromacs-4.5.3/src/kernel/grompp.c, line:
1356
Fatal error:
There were 9 errors in input file(s)
-------------------------------------------------------
I would be more than pleased if someone could guild me how to solve the
problem.
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