On Thu, Nov 15, 2012 at 3:47 PM, Justin Lemkul <[email protected]> wrote: > > > On 11/15/12 10:41 AM, Steven Neumann wrote: >> >> atomtypes.atp >> >> FE 55.84700 ; heme iron 56 >> >> ffnonbonded >> >> FE 9 18.998 0.000 A 0.115816833358244 -0 >> >> aminoacids.rtp >> >> [ FE ] >> [ atoms ] >> FE FE 2.00 0 >> >> >> Hmmmm, confusing... >> > > What force field is that? None of those parameters seem to come from any of > the default force fields in Gromacs. The entry in ffnonbonded is clearly > wrong, with the parameters appearing to belong to fluorine rather than iron, > but the line appears to have been mangled. It looks most like CHARMM, but > someone has messed with ffnonbonded.itp. > > Regardless, if you look at the parameters for FE in any of the force fields > in Gromacs, you will see that their nonbonded parameters (C6/C12 or > sigma/epsilon) are generally set to zero. They interact only via ionic > interactions because they were likely only intended for use in cofactors > like heme, where other bonded parameters fix their geometry. Using them as > free ions makes little sense. > > > -Justin >
This is charmm27 but modified as you can see. Shall I use: FE 26 55.84700 2.000 A 0.115816833358 0 0 in original Gromacs charmm it is FE 26 55.84700 0.000 A 0.115816833358 0.0 ; partial charge def not found > -- > ======================================== > > 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 > > ======================================== > -- > 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 -- 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
