Justin, Thank you very much. I assume that pairs in pairtypes are used to calculate 1-4 VdW interactions only and do not influence calculations of short range VdW?
Regards, km. On Wed, Aug 29, 2012 at 6:10 PM, Justin Lemkul <[email protected]> wrote: > > > On 8/29/12 11:37 AM, Krzysztof Murzyn wrote: > >> Hi, >> >> I want to influence slightly the way VdW interactions are calculated by >> providing customized values of sigma/epsilon in [ pairtypes ]. I employ >> OPLS/AA. The section of my molecule definition looks like, say: >> >> [ pairtypes ] >> CT CT 1 0.33 0.2 >> >> >> When I run grompp I get the following error message: >> >> Program grompp, VERSION 4.5.5 >> Source code file: toppush.c, line: 857 >> Fatal error: >> Atomtype CT not found >> >> >> What am I doing wrong? Overriding default definition of bondtypes, >> angletypes, or dihedraltypes works just fine. >> >> > All of those are bonded terms and use atomtype names that are translated > from their opls_* equivalents. In ffnonbonded.itp, you need to use opls_* > atomtypes. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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
