I found something in ffnonbonded in OPLSAA ff ; These ion atomtypes are NOT part of OPLS, but since they are ; needed for some proteins or tutorial Argon simulations we have added them. Cu2+ Cu2+ 29 63.54600 2.000 A 2.08470e-01 4.76976e+00 Fe2+ Fe2+ 26 55.84700 2.000 A 2.59400e-01 5.43920e-02 Zn2+ Zn2+ 30 65.37000 2.000 A 1.95200e-01 9.78219e-01 Ar Ar 18 39.94800 0.000 A 3.41000e-01 2.74580e-02
If they are not OPLS maybe it is possible to use them? Steven On Thu, Nov 15, 2012 at 4:34 PM, Steven Neumann <[email protected]> wrote: > On Thu, Nov 15, 2012 at 4:03 PM, Justin Lemkul <[email protected]> wrote: >> >> >> On 11/15/12 10:55 AM, Steven Neumann wrote: >>> >>> 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 >>> >> >> These changes will have no effect and will not solve your problem. The >> charge field in ffnonbonded.itp is never used for anything. I don't know >> what the extra zero is intended for, but it will probably break the ability >> of grompp to read the file. >> >> Moreover, the point of my previous comments was that your use of this atom >> type is not appropriate. The FE atom type still has zero repulsive >> interactions, unless explicitly calculated with each atom type. As far as I >> can tell from ffnonbonded.itp, this repulsive term is zero for every >> interaction, meaning no matter what you do, your Fe ions will always collide >> with something negatively charged because there are no LJ terms to impede >> the Coulombic attraction, leading to an infinitely negative potential at a >> fixed point and thus the crash. >> >> You need to find better parameters entirely if you wish to simulate free Fe >> ions. >> >> -Justin > > Thank you for this. I will try to look at Charmm forum for those > parameters. I was also thinking about parameters which Zn(2+) has got > as they have similar mass. What do you think? > > Steven > >> >> >> -- >> ======================================== >> >> 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
