Hi Justin I had taken United atom pdb file form PRODRG and i want to use OPLS-UA force field. i dont know what's wrong out there.I have done it befor for other molecules like DCE, CCL4 etc.
Regards Vinoth On Mon, Dec 20, 2010 at 11:01 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > vinothkumar mohanakrishnan wrote: > >> Hi all >> >> I want to use pdb2gmx to generate hexane topology and hexane.gro file. i >> have added the atom name in .atp file and corresponding section in .rtp >> file. i have given below my .rtp entry >> >> [ DRG ] >> [ atoms ] >> CAA opls_966 0 1 >> CAF opls_966 0 1 >> CAB opls_967 0 2 >> CAC opls_967 0 2 >> CAD opls_967 0 2 >> CAE opls_967 0 2 >> [ bonds ] >> CAA CAB >> CAB CAC >> CAC CAD >> CAD CAE >> CAE CAF >> [ angles ] >> CAA CAB CAC >> CAB CAC CAD >> CAC CAD CAE >> CAD CAE CAF >> [ dihedrals ] >> CAA CAB CAC CAD >> CAB CAC CAD CAE >> CAC CAD CAE CAF >> >> but i get the error message as given below and it doesn't generate any >> .top and .gro file . I searched the mailing list and found a similar post >> but there is no solution ( >> http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041609.html) >> previously i used pdb2gmx for other molecules and it worked fine for the >> oplsaa force field. any help is highly appreciated. >> >> Opening library file ffoplsaa.rtp >> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat >> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat >> WARNING: masses will be determined based on residue and atom names, >> this can deviate from the real mass of the atom type >> Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat >> Entries in atommass.dat: 178 >> WARNING: vdwradii will be determined based on residue and atom names, >> this can deviate from the real mass of the atom type >> Opening library file vdwradii.dat >> Entries in vdwradii.dat: 28 >> Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat >> Entries in dgsolv.dat: 7 >> Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat >> Entries in electroneg.dat: 71 >> Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat >> Entries in elements.dat: 218 >> Reading hexane.pdb... >> Read 6 atoms >> Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat >> 26 out of 26 lines of xlateat.dat converted succesfully >> Analyzing pdb file >> There are 1 chains and 0 blocks of water and 1 residues with 6 atoms >> >> chain #res #atoms >> 1 ' ' 1 6 >> All occupancies are one >> Opening library file ffoplsaa.atp >> Atomtype 1 >> Reading residue database... (ffoplsaa) >> Opening library file ffoplsaa.rtp >> >> ------------------------------------------------------- >> Program pdb2gmx, VERSION 4.0.7 >> Source code file: resall.c, line: 279 >> >> Fatal error: >> in .rtp file at line: >> >> >> ------------------------------------------------------- >> >> > There is something wrong with the format of your .rtp file. Unfortunately, > the error message in this case is not particularly helpful. > > Based on the residue and atom naming, it appears that you're trying to > interface some sort of PRODRG output with OPLS-AA. Doing so is > fundamentally flawed, mostly because PRODRG gives GROMOS-compatible > topologies (often poor ones, at that). Presumably, you have introduced new > atom types (opls_966/967) corresponding to some united-atom C type. OPLS-AA > is an all-atom force field, so introducing a united-atom hexane topology is > simply wrong, unless you have somehow demonstrated that a united-atom model > behaves properly and you have done the thorough work of parameterizing this > model. > > -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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