[gmx-users] grompp error for CNT simulation

[Justin A. Lemkul]

niaz poorgholami wrote:
> 
>  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.

atomtypes.atp is only read by pdb2gmx.  You need to introduce the proper 
nonbonded parameters for your new atom types in ffnonbonded.itp.

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================