Hi Justin I corrected the mistake what you said and i am able to run energy minimisation and equilibration. but when i view my em.gro and equilibration.gro in VMD it seems to me that the bonds between the atoms are broken in molecules.I used g_energy to check weather the system has equilibrated to the required temperature (300K) i found that the variation in the temperature was 100K (plus r minus) . i am not able find out what went wrong. any help is highly appreciated.
Regards Vinoth On Mon, Oct 18, 2010 at 6:09 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > vinothkumar mohanakrishnan wrote: > >> Dear Justin >> >> what corrections i should make to ffoplsaan.itp to make it correct. what i >> should give instead of CAB and CLAA?. >> >> > You must use atom types, not names. Unfortunately, you've chosen to use > atom names, which are also types, which makes all of this quite confusing if > you're not sure what you're doing. > > You defined two new atom types - opls_966 (CAB) and opls_967 (CLAA), which > are the only indicators you are allowed to use if introducing new types. > Thus, references to atom names (CAC, CLAD) will generate fatal errors. > > > 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)? >> >> > Your topology needs to be consistent with whatever files need to be > included. By default, Gromacs checks the working directory first, but if > you've moved to a new (sub)directory to carry out further steps, the grompp > will not find your modified files, but will instead locate only the default > force field files in $GMXLIB. Either keep all your work in one directory > (which can get messy), or make use of the "include" keyword in the .mdp > file. Any directory specified there will be searched after the working > directory, but before $GMXLIB. > > -Justin > > Regards >> Vinoth >> >> >> On Mon, Oct 18, 2010 at 5:27 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> 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 <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > 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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