AMBER Archive (2009)

Subject: Re: [AMBER] DMF solvent box

From: FyD (
Date: Thu Sep 17 2009 - 02:00:06 CDT


>                   Hi I have created the box at last. But I can't
> save the parameter as prmtop and inpcrd. For DMF its showing bond
> C-H1 not found ( the problem is H1 in C=O). I checked ff99..dat and
> I assigned atom type for DMF according to that in script.ff . plz
> help ME.\

Yes, you need to find an atom type for this alhehyde proton. Here you
have several choices.

1) You use antechamber to generate gaff atom types & the frcmod file
(if required), or
2) You use the HA atom type (capital letter) for this alhehyde proton
(C-HA bond), and you create FF parameters by analogy to CA-HA.
3) You create a new atom type HX for this alhehyde proton, and you
create the missing FF parameters involving HX by analogy to HA.

regards, Francois

AMBER mailing list