<br> Dear gmx users,<br>I am using gromacs 4.5.3 to simulate CNT in water. up to now I have done<br>these things:<br>1. I used packmol to create my PDB file and the used editconf to change PDB to gro file.<br>2. I copied oplsaa.ff folder in my working directory<br>
3. I added following lines to atomname2type.n2t<br>C opls_995 0 12.011 2 C 0.142 C 0.142<br>C opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142<br>C opls_997 0 12.011 4 C 0.142 C 0.142 C 0.142 C 0.142<br>
C opls_998 0 12.011 5 C 0.142 C 0.142 C 0.142 C 0.142 C 0.142<br>4. I added these to atomtypes.atp<br> opls_995 12.01100 <br> opls_996 12.01100 <br> opls_997 12.01100 <br> opls_998 12.01100 <br>
<br>5. I added these to ffbonded.itp<br>[ bondtypes ]<br> C C 1 0.14210 478900<br><br> [ angletypes ]<br> C C C 1 120.000 397.480<br><br>[ dihedraltypes ]<br> C C 1 0.000 167.360 1<br>6. I used g_x2top to create topology for CNT.<br>
Command line was:<br><br>g_x2top -f CNT.gro -o CNT.top -pbc -nopairs -name CNT -nexcl 5<br><br>7. I wrote a .top file given below,<br>; Include forcefield parameters<br>#include "./oplsaa.ff/forcefield.itp"<br>; Include topology for water<br>
#include "oplsaa.ff/spc.itp"<br>; Include topology for CNT<br>#include "oplsaa.ff/CNT.itp"<br><br>[ system ]<br>; Name<br>SDS and CNT in water<br>[ molecules ]<br>; Compound #mols<br>water 9000<br>
CNT 1<br>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<br>it gave me the following error:Atomtype opls_995 not found.<br> I would be pleased if anyone could help me how to fix this.<br>
niaz<br><br><br><br>