AMBER Archive (2006)

Subject: AMBER: failed to save prm and xyz using ff96

From: Abd Ghani Abd Aziz (
Date: Tue Feb 28 2006 - 09:32:49 CST

Dear amber users,

I want to run MD for my protein with two metal atoms
(Zn and Ca). somebody created for me the zn.lib and
ca.lib. Then i load these two files in the xleap but i
failed to save the prm and xyz files. However, when
using the ff03, it perfectly works.

Below are the steps that i did in the xleap:-

>source leaprc.ff96
>loadoff ca.lib
>loadoff zn.lib
>b=loadPDB leow.pdb

>solvateoct b TIP3PBOX 10.0 iso
>check b
 (the charge is -2) - unit is ok - no error

>addions b Na+ 0
>saveamberparm b t1.prm
checking unit
building topology
building atom parameters
For atom: .R<Zn 389>.A<ZN1 1> Could not find type: Zn
For atom: .R<C0 390>.A<CA1 1> Could not find type: C0
Parameter file was not saved.

from the error i know the errors come from metal that
included in the pdb (below).

ATOM 3058 ZN1 zn M 389 21.420 11.364 38.672
ATOM 3059 CA1 ca N 390 -8.398 -2.975 28.440

i've changed the pdb to this :

ATOM 3058 ZN1 Zn M 389 21.420 11.364 38.672
ATOM 3059 CA1 C0 N 390 -8.398 -2.975 28.440

but it still does not work for me... i hope that
somebody can help me.. thanks

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