Dear Justin what corrections i should make to ffoplsaan.itp to make it correct. what i should give instead of CAB and CLAA?.
i copied the .rtp .atp .itp files from usr/local/gromacs/share/gromacs/top to my working directory and added these parameters to the corresponding files. what you mean is should i need to add these parameters to the source directory ( usr/local/gromacs/share/gromacs/top)? Regards Vinoth On Mon, Oct 18, 2010 at 5:27 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > vinothkumar mohanakrishnan wrote: > >> Hi all >> >> i added new atomtype for dichloroethane (DCE) and added the corresponding >> parameters in the .rtp, .atp, .bon.itp, .nb.itp respectively. given below >> are my additions to the corresponding files respectively. >> >> *ffoplsaa.rtp* >> >> [ DCE ] >> [ atoms ] >> CLAA opls_967 -0.2270 1 >> CAB opls_966 0.2270 1 >> CAC opls_966 0.2270 2 >> CLAD opls_967 -0.2270 2 >> >> [ bonds ] >> CLAA CAB >> CAB CAC >> CAC CLAD >> >> [ angles ] >> CLAA CAB CAC >> CAB CAC CLAD >> >> [ dihedrals ] >> CLAA CAB CAC CLAD >> >> *ffoplsaa.atp* >> >> opls_966 14.02700 ; CH2 for DCE >> opls_967 35.45300 ; CL for DCE >> >> *ffoplsaabon.itp* >> >> [bondtypes] >> CLAA CAB 1 0.17870 194137.6 ; CL-CH2 for DCE >> CAB CAC 1 0.15300 259408.0 ; CH2-CH2 for DCE >> CAC CLAD 1 0.17870 194137.6 ; CL-CH2 for DCE >> >> [angletypes] >> CLAA CAB CAC 1 108.200 368.192 ; C-C-CL for DCE >> CAB CAC CLAD 1 108.200 368.192 ; C-C-CL for DCE >> >> [dihedraltypes] >> CLAA CAB CAC CLAD 3 20.76096 -0.4184 27.011904 0.00000 >> 0.00000 0.00000 ; for DCE >> >> > You shouldn't be using atom names in the [*types] directives. What you > should be using are the interpolated types from ffoplsaanb.itp, thus you > have only utilized opls_966 (CAB) and opls_967 (CLAA). > > *ffoplsaanb.itp* >> >> >> opls_966 CAB 6 14.02700 0.227 A 3.98000e-01 >> 4.76976e-01 ; CH2 of DCE >> opls_967 CLAA 17 35.45300 -0.227 A 3.16000e-01 >> 0.20920e+01 ; Cl of DCE >> >> *dce.pdb* >> >> HETATM 1 CLAA DCE 1 6.300 -2.280 1.360 1.00 20.00 >> CL >> HETATM 2 CAB DCE 1 5.060 -3.540 1.500 1.00 20.00 >> C >> HETATM 3 CAC DCE 1 4.320 -3.740 0.170 1.00 20.00 >> C >> HETATM 4 CLAD DCE 1 3.270 -2.350 -0.210 1.00 20.00 >> CL >> >> After adding all this, when i run grompp i get the error as *fatal error >> Unknown bond_atomtype CLAA*. can any one tell me why this happens?. >> >> > Have you been sure to #include the correct (modified) force field files? > That is, if you made a local copy and adjusted them, these won't be the > files that pdb2gmx will #include by default. > > -Justin > > Regards >> Vinoth >> >> > -- > ======================================== > > 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 > > ======================================== > -- > 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 >
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