> 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
