[gmx-users] overlapped parameters

[Justin Lemkul]

On 11/21/17 4:48 AM, Albert wrote:
> Hello,
>
> 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 
> consecutive
>   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

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================