Dear Mark I generated the topology using pdb2gmx using dce.pdb. i checked the .top file and i contains necessary .itp files. the error message that i get is given below. any help is highly appreciated.
Program grompp, VERSION 4.0.7 Source code file: toppush.c, line: 620 Fatal error: Unknown bond_atomtype CLAA Regards Vinoth On Mon, Oct 18, 2010 at 5:12 PM, Mark Abraham <[email protected]>wrote: > On 18/10/2010 10:31 PM, 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 > > *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?. > > > I can't tell until I know how you've invoked grompp, and how you generated > the .top file it needs, and which line of that .top grompp doesn't like. > When asking for help, please copy and paste all your relevant commands, and > any error messages in full, and any relevant chunk of the .top. Check > whether that .top file is #including the correct .itp files. > > Mark > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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