[gmx-users] overlapped parameters
jalemkul at vt.edu
Tue Nov 21 16:29:05 CET 2017
On 11/21/17 4:48 AM, Albert wrote:
> I have set my topol.top file as following:
> ; Include forcefield parameters
> #include "charmm36-jul2017.ff/forcefield.itp"
> #include "input/unk.prm"
> #include "input/unk.itp"
> Then I run grompp command line. I obtained the following warnings:
> WARNING 1 [file unk.prm, line 22]:
> Overriding Proper Dih. parameters.
> Use dihedraltype 9 to allow several multiplicity terms. Only
> lines are combined. Non-consective lines overwrite each other.
> old: 0 8.7864 1 0 8.7864 1
> new: CG2R61 CG311 OG311 HGP1 9 0.000000
> 5.857600 2
> I am just wondering will Gromacs use the parameters from
> "charmm36-jul2017.ff/forcefield.itp" or from "input/unk.prm" ?
It uses whatever it finds last, which presumably is the ligand
parameters. You don't want that. If an interaction is already
specifically parametrized in the force field, you do not want to
override it with something generic and therefore less accurate. Delete
any duplicate parameters from the inhibitor parameter file.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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