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