Dear all I am using Gromacs 4.5.3 to simulate a system including: CNT+water+surfactant and I want to use opls force field for my whole system. so far I have done following things: 1.I copied oplsaa.ff folder in my working directory. 2.I added following lines to atomname2type.n2t C opls_995 0 12.011 1 C 0.142 C opls_996 0 12.011 2 C 0.142 C 0.142 C opls_997 0 12.011 3 C 0.142 C 0.142 C 0.142 C opls_998 0 12.011 4 C 0.142 C 0.142 C 0.142 C 0.142 3.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 4.I added these to ffnonbonded.itp opls_995 C 6 12.01100 0.000 A 3.851000e-01 4.39600e-01 opls_996 C 6 12.01100 0.000 A 3.851000e-01 4.39600e-01 opls_997 C 6 12.01100 0.000 A 3.851000e-01 4.39600e-01 opls_998 C 6 12.01100 0.000 A 3.851000e-01 4.39600e-01 5.I used g_x2top to create topology for CNT. Command line was: g_x2top -f cnt.pdb -o cnt.top -r cnt.rtp -name CNT -nexcl 5 6.I used TopolGen to produce the *.itp file for surfactant molecule. 7.I placed surfactant molecules around CNT. 8.I used editconf using this command: editconf -f cnt_sur.pdb -o cnt_sur.gro -c -d 1 -bt cubic 9. I wrote a a .top file given below, Include forcefield parameters #include "./oplsaa.ff/forcefield.itp" ; Include topology for DTAB #include "DTAB.itp" ; Include topology for CNT #include "cnt.itp" ; [ molecules ] ; molecule name nr. DTAB 14 CNT 1 10.I called genbox with the command: genbox -cp cnt_sur.gro -cs spc216.gro -p topol.top -o solv.gro 11.I added manually these to topol.top ; Include SPC water topology #include "oplsaa.ff/spc.itp" 12. once I run grompp : grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr I got following errors: Ignoring obsolete mdp entry 'title' WARNING 1 [file ffbonded.itp, line 2704]: Overriding Bond parameters. old: 0.151 292880 0.151 292880 new: C C 1 0.14210 478900 Generated 335790 of the 335790 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 335790 of the 335790 1-4 parameter combinations ERROR 1 [file DTAB.itp, line 104]: No default Bond types ERROR 2 [file DTAB.itp, line 105]: No default Bond types ERROR 3 [file DTAB.itp, line 241]: No default Angle types ERROR 4 [file DTAB.itp, line 242]: No default Angle types ERROR 5 [file DTAB.itp, line 244]: No default Angle types ERROR 6 [file DTAB.itp, line 245]: No default Angle types ERROR 7 [file DTAB.itp, line 249]: No default Angle types ERROR 8 [file DTAB.itp, line 302]: No default Ryckaert-Bell. types ERROR 9 [file DTAB.itp, line 303]: No default Ryckaert-Bell. types Excluding 3 bonded neighbours molecule type 'DTAB' Excluding 5 bonded neighbours molecule type 'CNT' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 27]: System has non-zero total charge: 5.039999e+00 There was 1 note There was 1 warning ------------------------------------------------------- Program grompp, VERSION 4.5.3 Source code file: /build/buildd/gromacs-4.5.3/src/kernel/grompp.c, line: 1356 Fatal error: There were 9 errors in input file(s) ------------------------------------------------------- I would be more than pleased if someone could guild me how to solve the problem.
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