RE: AMBER: trajin and rms

From: a a <>
Date: Wed, 24 May 2006 18:49:05 +0800

Dear Sir/Madam,

I am trying calculate the binding energy of a Pt-complex with protein and

I am wondering if I should use the approach as Tutorial one, i.e.

$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99

However, when I do it, and load the Pt-complex, I found it did not said Pt
is unknown atom, does it mean that we got parameters for Pt? however, when
I lookup the window, the structure looks strange.

If not, should I use the approach in tutorial five, i.e. antechamber? It
tried it once, since my complex is +2 charged, how can I incorporate this to
the calculation?

It seems to me that it is only applicable for organic compounds, is it work
for Pt-complex?

Please kindly help. Many thanks in advanced.

Best regards,


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Received on Fri May 26 2006 - 21:05:17 PDT
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