AMBER Archive (2004)

Subject: Re: AMBER: questions on dummy atom types in FEP setup

From: Chunhu Tan (tanc_at_uci.edu)
Date: Mon Nov 22 2004 - 17:37:57 CST

 Hi, Eric,

    I think you should add NONBON term in your frcmod, like:

NONBON
  DH 0.0 0.0
  DC 0.0 0.0

Regards,
Chunhu
----- Original Message -----
From: "Eric Hu" <yhu_2003_at_yahoo.com>
To: <amber_at_scripps.edu>
Sent: Monday, November 22, 2004 1:37 PM
Subject: AMBER: questions on dummy atom types in FEP setup

> Hi, I try to set up a FEP calculation by perturbing a
> small organic
> molecule to nothing in water and protein later.
> However I keep getting
> errors on the defined dummy atom types. Here is part
> of the table using "edit selected atoms" from xleap.
>
> Name Type Charge Element Unused PERT.name PERT.type
> Delta.charge
C01 c3 0.0244 C true DC1
dc 0.000
H09 hn 0.1856 H true DH9
dh 0.000
> ...
>
> I use gaff atom types calculated by antechamber. The
> frcmod file looks
> like this:
>
> MASS
> dh 1.0 0.0
> dc 12.0 0.0
> dn 14.0 0.0
> do 16.0 0.0
>
> BOND
>
> ANGLE
>
> DIHE
>
> Here is the error when I try to save the perturbed top
> and crd files.
>
> For atom: .R<ts1 0>.A<C01 1> type c3
> Could not find perturbed type: dc
> For atom: .R<ts1 0>.A<C02 2> type c3
> Could not find perturbed type: dc
> For atom: .R<ts1 0>.A<C04 4> type c3
> Could not find perturbed type: dc
> ...
>
>
>
> Eric
>
>
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