2
$\begingroup$

I am trying to parameterize a molecule. I know dihedrals and impropers are the same for Amber Force Field. (Source: http://archive.ambermd.org/201004/0334.html) So, I did PET scan for improper and I found this chart:

enter image description here

According to this chart and Amber7 manual Appendix-C I should define impropers like this in my mini-force field:

C-O-B-C 40.5 180.0 2.0

But in gaff and gaff2 the biggest improper values are not greater than 15 ( here is gaff2: https://github.com/choderalab/ambermini/blob/master/share/amber/dat/leap/parm/gaff2.dat and here is gaff: https://github.com/choderalab/ambermini/blob/master/share/amber/dat/leap/parm/gaff2.dat)

And to compare my improper values with gaff, I scanned C-C-C-C impropers and I obtained almost the same chart as above but in gaff, this improper is defined like this:

C-C-C-C 1.1 180.0 2

(line 6693 : https://github.com/choderalab/ambermini/blob/master/share/amber/dat/leap/parm/gaff2.dat#L6693)

so it is obvious gaff doesn't use PES scan values for improper but it seems unreasonable because dihedral values fits with PES scan. So what should I do? Should I use values which I obtained from PES scan ( C-O-B-C 40.5 180.0 2.0) or what should I do?

Improve this question
$\endgroup$
5
  • 1
    $\begingroup$ Amber has a mailing list for these types of questions where the creators of GAFF will be answering your question. Also, Amber7 is old. They are at least at Amber18 now. $\endgroup$ – B. Kelly Feb 24 '19 at 20:20
  • 2
    $\begingroup$ @charlie it has nothing to do with ambertools version and gaff. from amber 4 to amber 18 force field definition hasn't changed. $\endgroup$ – Erdem Caner Feb 25 '19 at 20:50
  • 2
    $\begingroup$ There are a few reasons I don't use windows 95 anymore $\endgroup$ – B. Kelly Feb 25 '19 at 20:57
  • 2
    $\begingroup$ "force field parameterization" is not a software. it is a basic rule like f=m*a $\endgroup$ – Erdem Caner Feb 25 '19 at 22:13
  • 1
    $\begingroup$ in amber7 and amber16 manuals, parameter definitions are the same one to one. in amber16 manual page 230s and in amber7 manual appendix-C. and other amber manual page bla bla about parameters are the same. something never changes. (also amber has no windows version) . $\endgroup$ – ANIL FRINGE Feb 25 '19 at 22:35

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.