AMBER Archive (2006)

Subject: AMBER: Pt containing complex: antechamber

From: a a (patd_2_at_hotmail.com)
Date: Sun May 28 2006 - 22:42:31 CDT

Dear Sir/madam.

I am trying to do a MD calculation for a Pt containing complex. I tried to
run the antechamber to creat leap input files. Is it the right thing to use
antechamber for inorganic complex? The following is the error messages that
I encountered.

[PATH]$ $AMBERHOME/exe/antechamber -i Pt_nopi.pdb -fi pdb -o Pt_nopi.prepin
-fo prepi -c bcc -s 2
Running: /PATH/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC -o
ANTECHAMBER_BOND_TYPE.AC -f ac -j full

Bond types are assigned for valence state 1 with penalty of 1

Running: /PATH/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p
gaff

Total number of electrons: 177; net charge: 0
Number of electrons is odd: 177
Please check the total charge and your -nc flag

The complex that I am doing now is Pt(II) with four aromatic ligand. How
can I define the +2 in the Pt. As it seems to be the error message related.
  Besides, did I still miss any important things here?

Please kindly help.

Best regards,

aa

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