I am re-reading the email from Yigitcan and I'm not sure why the program
would not detect the SH CT CX C torsion. It may be that, while all of
these atom types are present in the topology, the parm.dat and frcmod files
contain SH-CT bonds and SH-CT-CX angles but no examples of the SH-CT-CX-C
torsion itself. One thing to try might be to look at the HB2 / HB3
hydrogen atom types and see if the torsions between C CX CT and [ HB2 / HB3
type ] can be parameterized. This is not a general solution, but it would
shed light on the problem.
Parameter fitting is a tough problem, and if I could retire mdgx in favor
of a different implementation, I would. The plain C framework mdgx is
written in doesn't permit the ease of error checking that I would like, and
there is so much that can go wrong in the parameter files, which are
probably the least bulletproofed of the Amber file formats. There are only
a handful of programs that read the things and most of them are used by
only a few researchers in one work group. In time the new code base I am
developing will be on its feet, and I may be able to take my "google 20%"
to swing back to this parameter fitting problem in a new and more powerful
way. If I could wave a magic wand, mdgx would have a few hundred unit
tests for just the parameter fitting module, but this is what I've learned
in the ten years since I started down that path.
Dave
On Sat, Apr 2, 2022 at 12:20 AM Erdem Yeler <erdemyeler.gmail.com> wrote:
> >
> >
> > Personally, I couldn't use mdgx because of the same problem. I changed
> > amber atom masks and tried new ways again and again, but I couldn't.
> > Then I wrote my own script to generate dihedrals. Perhaps you should
> > contact the mdgx developer (D.S. Cerutti) directly. I am sure he will
> > answer.
> >
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Received on Tue Apr 05 2022 - 16:30:03 PDT
