[gmx-users] dihedral restraints
Jessica Leuchter
jessica.leuchter at gmail.com
Mon Mar 23 16:29:51 CET 2015
Do you also change the angle to where you want to constrain it to? Or just
the kfac?
On Mon, Mar 23, 2015 at 5:27 PM, Andrew Ritchie <drew.w.ritchie at gmail.com>
wrote:
> "It will depend on the force field parameters for each set of 4 atoms and
> how much or little you want to allow them to fluctuate."
> I forgot to mention, the local environment also matters.
>
> On Mon, Mar 23, 2015 at 10:23 AM, Andrew Ritchie <drew.w.ritchie at gmail.com
> >
> wrote:
>
> > It will depend on the force field parameters for each set of 4 atoms and
> > how much or little you want to allow them to fluctuate. If you want to
> > allow some movement, some experimentation is required. If you want them
> to
> > essentially not move, just chose an arbitrarily large number. When I
> want
> > to remove essentially all dihedral movement, I typically choose ~ 1000
> > (kJ/mol/rad^2) and see very little movement. When I'm doing umbrella
> > sampling about a dihedral, I typically use 50-70 (kJ/mol/rad^2).
> >
> > On Mon, Mar 23, 2015 at 9:47 AM, Jessica Leuchter <
> > jessica.leuchter at gmail.com> wrote:
> >
> >> To get the dihedrals to stay restrained to their original values what
> >> should the kfac be?
> >>
> >> On Fri, Mar 20, 2015 at 3:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >> >
> >> >
> >> > On 3/20/15 9:00 AM, Jessica Leuchter wrote:
> >> >
> >> >> Dear All,
> >> >>
> >> >> I would like to add dihedral restraints to 10 residues in my topology
> >> >> file using the newest version of gromacs. I have done the
> >> >> following(see below) to my topology file. And this is the *grompp
> >> >> command* I am using: gmx grompp -f ions.mdp -c 1AKI_solv.gro -p
> >> >> topol.top -o ions.tpr. But I am getting the error message below.
> >> >>
> >> >> *topol.top file*:
> >> >>
> >> >> [ dihedral_restraints ]
> >> >> ; ai aj ak al fnID phi dphi kfac
> >> >>
> >> >> 1497 1499 1509 1511 9 -70.488 0 1
> >> >> 1499 1509 1511 1513 9 -12.561 0 1
> >> >> 1511 1513 1515 1518 9 95.706 0 1
> >> >> 1513 1515 1518 1520 9 -117.614 0 1
> >> >> 1518 1520 1522 1530 9 -111.163 0 1
> >> >> 1520 1522 1530 1532 9 -72.034 0 1
> >> >> 1530 1532 1534 1542 9 -108.627 0 1
> >> >> 1532 1534 1542 1544 9 -103.437 0 1
> >> >> 1542 1544 1554 1556 9 -80.981 0 1
> >> >> 1544 1554 1556 1558 9 46.231 0 1
> >> >> 1556 1558 1560 1570 9 -107.016 0 1
> >> >> 1558 1560 1570 1572 9 20.452 0 1
> >> >> 1570 1572 1574 1587 9 -82.626 0 1
> >> >> 1572 1574 1587 1589 9 169.300 0 1
> >> >> 1587 1589 1591 1608 9 -82.868 0 1
> >> >> 1589 1591 1608 1610 9 -47.555 0 1
> >> >> 1608 1610 1612 1623 9 -39.285 0 1
> >> >> 1610 1612 1623 1625 9 -72.644 0 1
> >> >> 1623 1625 1627 1642 9 -7.261 0 1
> >> >> 1625 1627 1642 1644 9 -51.880 0 1
> >> >> 1642 1644 1646 1652 9 -38.845 0 1
> >> >> 1644 1646 1652 1654 9 -73.856 0 1
> >> >>
> >> >>
> >> >> *Fatal error:*
> >> >> Incorrect number of parameters - found 2, expected 3 or 6 for Dih.
> >> Rest..
> >> >> For more information and tips for troubleshooting, please check the
> >> >> GROMACS
> >> >> website at http://www.gromacs.org/Documentation/Errors
> >> >>
> >> >>
> >> > Your restraints directive uses the wrong format. See manual section
> >> > 5.7.1, which has a complete example of dihedral restraints and an
> >> > explanation of all the required columns.
> >> >
> >> > -Justin
> >> >
> >> > --
> >> > ==================================================
> >> >
> >> > Justin A. Lemkul, Ph.D.
> >> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >> >
> >> > Department of Pharmaceutical Sciences
> >> > School of Pharmacy
> >> > Health Sciences Facility II, Room 629
> >> > University of Maryland, Baltimore
> >> > 20 Penn St.
> >> > Baltimore, MD 21201
> >> >
> >> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> > http://mackerell.umaryland.edu/~jalemkul
> >> >
> >> > ==================================================
> >> > --
> >> > Gromacs Users mailing list
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> >> >
> >>
> >>
> >>
> >> --
> >> Jessica Leuchter
> >> Wake Forest University 2014
> >> 954.591.2222
> >> --
> >> Gromacs Users mailing list
> >>
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> >>
> >
> >
> >
> > --
> > -Andrew Ritchie
> >
>
>
>
> --
> -Andrew Ritchie
> --
> Gromacs Users mailing list
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--
Jessica Leuchter
Wake Forest University 2014
954.591.2222
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