I have tested your molecule using your prepin and frcmod files. I also did
igb=1 minimization for 10,000 steps. I did not observe weird behavior of
amide groups. Please check if you can reproduce my result.
All the best
Junmei
On Wed, Apr 29, 2020 at 4:44 AM Arnaud Bondon <arnaud.bondon.univ-rennes1.fr>
wrote:
> Hi,
>
> Thanks for the two responses.
>
> About solvent I only used igb=1 when performing simulated annealing
> under NMR restraints (sa.in)
>
> The prep directory is attached.
>
> Many thanks for your help
>
> sincerely
>
> arnaud
>
> Le 28/04/2020 à 23:02, Junmei Wang a écrit :
> > Gaff adopted the good parameters from amber biomolecular force field. So
> > the peptide-like parameters should be similar. For you minimization, did
> > you consider solvent effect? If you send me your prep file, I will check
> if
> > it is a force field issue or not.
> >
> > Best
> >
> > Junmei
> >
> > On Fri, Apr 24, 2020 at 11:02 AM David A Case <david.case.rutgers.edu>
> > wrote:
> >
> >> On Fri, Apr 24, 2020, Arnaud Bondon wrote:
> >>
> >>> ). Clearly the N10 amide nitrogen
> >>> has an pyramidal character. And the omega dihedral angles are not good
> >>>
> >>> The molecule was prepared as a mol2 file Nitrogen are N.am
> >> The input atoms types don't matter: you should look at the output types
> >> in the prep file. If this is a peptide-like molecule, it may be that
> >> the gaff types don't do as well as the tuned Amber atom types.
> >> You might want to see what happens if you request Amber atom types.
> >>
> >> I'm not sure whether GAFF has types that are specifically tuned for
> >> peptide bonds or not...cc-ing Junmei here.
> >>
> >> ...good luck...dac
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> POUR UNE RECONNAISSANCE DE LA PALESTINE DANS LES FRONTIERES DE 1967
> OU UN ETAT COMMUN
>
> Arnaud BONDON
> Equipe CORINT, UMR CNRS 6226
> PRISM
> CS 34317
> Campus de villejean
> Université de Rennes 1
> 35043 RENNES Cedex France
> tel: (0)2 23 23 65 61
> arnaud.bondon.univ-rennes1.fr
> http://iscr.univ-rennes1.fr
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 29 2020 - 07:30:02 PDT
