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
i'm
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
>plc=b
>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 t2.xyz
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).
TER
ATOM 3058 ZN1 zn M 389 21.420 11.364 38.672
TER
ATOM 3059 CA1 ca N 390 -8.398 -2.975 28.440
TER
END
i've changed the pdb to this :
TER
ATOM 3058 ZN1 Zn M 389 21.420 11.364 38.672
TER
ATOM 3059 CA1 C0 N 390 -8.398 -2.975 28.440
TER
END
but it still does not work for me... i hope that
somebody can help me.. thanks
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Received on Sun Mar 05 2006 - 06:10:10 PST
