[gmx-users] grompp error for CNT simulation

niaz poorgholami poorgholami at gmail.com
Sat Dec 3 08:16:03 CET 2011


 Dear gmx users,
I am using gromacs 4.5.3 to simulate CNT in water. up to now I have done
these things:
1. I used packmol to create my PDB file and the used editconf to change PDB
to gro file.
2. I copied oplsaa.ff folder in my working directory
3. 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
4. I added these to atomtypes.atp
 opls_995   12.01100
 opls_996   12.01100
 opls_997   12.01100
 opls_998   12.01100

5. 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
6. I used g_x2top to create topology for CNT.
Command line was:

g_x2top -f CNT.gro -o CNT.top -pbc -nopairs -name CNT -nexcl 5

7. I wrote a .top file given below,
; Include forcefield parameters
#include "./oplsaa.ff/forcefield.itp"
; Include topology for water
#include "oplsaa.ff/spc.itp"
; Include topology for CNT
#include "oplsaa.ff/CNT.itp"

[ system ]
; Name
SDS and CNT in water
[ molecules ]
; Compound        #mols
water               9000
CNT                 1
8. when I run grompp  for EM with this command line :grompp -f md.mdp -c
cnt_alone.gro -p topol.top -o em.tpr
it gave me the following error:Atomtype opls_995 not found.
 I would be pleased if anyone could help me how to fix this.
                                   niaz
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