AMBER Archive (2009)

Subject: Re: [AMBER] non standart residue library creation with tleap (Zn atom)

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Nov 23 2009 - 11:31:31 CST

Quoting Andrew Voronkov <drugdesign_at_yandex.ru>:

> 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 @
http://q4md-forcefieldtools.org/Help/Andrew/

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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