[gmx-users] Re: grompp error for CNT simulation

[Dr. Vitaly V. Chaban]

>  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.


Maybe the non-found atomtype is really absent? On the gromacs website,
there should be some examples for the CNT topologies based on the
GROMOS FF.

Independently, check your angles once again. It seems, there should be
more angles which are to be defined for a tube.


Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA