AMBER Archive (2006)

Subject: RE: AMBER: trajin and rms

From: a a (patd_2_at_hotmail.com)
Date: Wed May 24 2006 - 05:49:05 CDT

Dear Sir/Madam,

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

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,

Annie

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