VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Tue Oct 03 2017 - 17:21:52 CDT

OG2D1 is (typically) an atom type, so it’s fine to be repeated. I doubt it’s the name, which would be in the first column (type in the second) of the topology (str) file.

FFTK doesn’t treat impropers (we’ve found their actually relatively easy/better to do by hand anyway). So any improper must be coming from paramchem. Are you also loading the cgenff parameter file? “str” stands for “stream”, meaning that you still usually need a parent cgenff parameter file to go with it. Maybe the improper is in there?

Best,
JC

> On Oct 3, 2017, at 6:44 AM, RAHUL SURESH <drrahulsuresh_at_gmail.com> wrote:
>
> During my dihedral optimisation,
>
> The error call is as follows
>
> FATAL ERROR: BAD IMPROPER FORMAT IN CHARMM PARAMETER FILE
> LINE=*CG2O1 CG301 NG2S1 OG2D1 0.0000 ! *
>
> Earlier i had an error stating
>
> Charm++ fatal error:
> FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2O1 CG301 NG2S1 OG2D1 (ATOMS 12 7 14 13)
>
> So I manually added the improper angle to the parameter file.
>
> I note that two oxygen atom in the molecule are having same name OG2D1. The naming was done from the str file generated using cgenff.parachem server.
>
> Thanks in advance
>
> --
> Regards,
> Rahul Suresh
> Research Scholar
> Bharathiar University
> Coimbatore