AMBER: Problems loading parameter file in tleap

From: Eduardo Mendez <>
Date: Fri, 21 Sep 2007 04:58:48 -0600

Greetings Amber users.

I have this interesting not quite welcome issue:
when I load my parameter file and the pdb file the following output

CMPLX=loadPdb AQUI.pdb
Loading PDB file: ./AQUI.pdb
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C1-C2-*
+--- With Sp0 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
 total atoms in file: 6
> check CMPLX
Checking 'CMPLX'....
WARNING: The unperturbed charge of the unit: -2.000000 is not zero.
Checking parameters for unit 'CMPLX'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.
> quit

The unit however is okay. Any ideas?.

I am doing Oxalate, and yes, the charge is supposed to be -2.
Should I try to combine atom types in a different fashion?.
Carbons are C1, Oxygens are O2 type

Thanks for the input!

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Received on Sun Sep 23 2007 - 06:07:40 PDT
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