AMBER Archive (2009)
Subject: Re: [AMBER] non standart residue library creation with tleap (Zn atom)
From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Mon Nov 23 2009 - 11:38:28 CST
How to create frcomd file then? Manually?
- how was this frcmod file created? Where should I get bond and dihedrals parameters then, to measure them in the protein or to make estimation by some software?
I don't quite understand how Ross Walker has made that frcmod file.
23.11.09, 18:31, "FyD" <fyd_at_q4md-forcefieldtools.org>:
> Quoting Andrew Voronkov :
> > This is kind of zinc finger and it is connected to four amino acids,
> > not small molecule ligands. So in case of amino acids I should also
> > define frcmod for this zinc atom and four amino acids which are
> > bound to it? To construct frcmod file by antechamber or use the
> > frcmod file which I've mentioned above?
> > And the library in this case (saveoff zinc.lib) should also be
> > defined for the zinc atoms and four amino acids to which it is
> > connected, right?
> If you want to consider the whole complex i.e. Zinc-connected to
> amino-acids, you canNOT use what is available @
> You need to create a frcmod file + an off FF library for your Zn-amino
> acid complex.
> my mistake:
> I do NOT think Antechamber handles metal atoms.
> regards, Francois
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