I will try. Thank you soo much for your valuable answer.
David Case <david.case.rutgers.edu>, 5 Oca 2020 Paz, 21:42 tarihinde şunu
yazdı:
> On Sun, Jan 05, 2020, Erdem Yeler wrote:
>
> >I parameterized some novel molecules for AMBER but it is very strange that
> >when I use gaff atom types in the mol2 and frcmod file, minimized geometry
> >moves away from the real X-ray structure... but when I use with the
> >--almost-- same parameters with the AMBER Atom type (you know, ouput from
> >parmchk2 without any flag, capital letters frcmod file) I am getting
> really
> >good results.
>
> Run two single-point calculations, using identical input coordinates, but
> with the two different prmtop files. Are any of the components of the
> energy the same? Do the differences suggest any ideas?
>
> You can also use parmed to see all the force field terms involving any
> subset of atoms (such as "M"). Do that with both prmtop files, and see
> if you can spot differences.
>
> Some combination of these ideas should help you find the source of the
> difference between the two files. I note that you are using "O" (rather
> than "OS" as the analogue of "os" is gaff. Maybe the prmtop file has
> picked up some component of "O" (not in the parmchk file) that is quite
> different from "os". [This is just a guess, since I don't know how much
> you you cut out of the frcmod files.]
>
> ....dac
>
>
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Received on Tue Jan 07 2020 - 00:30:01 PST
