Dear Justin, Regarding our previous discussion under "CNT" topic, you want to know exactly what I did to define C-C interaction. I have summarized it below.
1. I copied oplsaa.ff folder in my working directory 2. 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 3. I added those to atomtypes.atp opls_995 12.01100 ; opls_996 12.01100 ; opls_997 12.01100 ; opls_998 12.01100 ; 4. I added those to ffbonded.itp [ bondtypes ] C C 1 0.14210 478900 [ angletypes ] C C C 1 120.000 562.2 [ dihedraltypes ] 5. I constructed .top file for CNT with the following, then I converted it into .itp by vi editor g_x2top -f cnt.gro -o cnt.top -nopairs -nexcl 5 6. By pdb2gmx, I obtained .top for peptide then I converted it into .itp 7. I combined CNT and peptide's pdbs in pymol and saved. 8. I wrote a .top file given below, ; ; File 'topol.top' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Mon Jan 10 02:51:19 2011 ; ; This is a standalone topology file ; ; It was generated using program: ; pdb2gmx - VERSION 4.5.3 ; ; Command line was: ; pdb2gmx -ignh -f vpgvg10.pdb ; ; Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include "forcefield.itp" ; Include topology for CNT #include "cnt.itp" ; Include topology for UW1 #include "uw1.itp" ; Include water topology #include "spc.itp" [ system ] ; Name Protein and CNT in water [ molecules ] ; Compound #mols Protein 1 CNT 1 SOL 4019 9. When I make grompp for minimization it givea me the following error WARNING 1 [file ffbonded.itp, line 2703]: Overriding Bond parameters. old: 0.151 292880 0.151 292880 new: C C 1 0.14210 478900 ERROR 1 [file ffbonded.itp, line 2707]: Not enough parameters Generated 334153 of the 334153 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 334153 of the 334153 1-4 parameter combinations ------------------------------------------------------- Program grompp, VERSION 4.5.3 Source code file: toppush.c, line: 1166 Fatal error: Atomtype opls_996 not found That is all what I exactly did. Is anything wrong or missing? best wishes trevor
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