Hi Amber Users
I am using Antechamber module of Amber 9.0 for preparing the prepi file for
my compound.
I gave the following command
antechamber -i ionic.log -fi gout -o ionic.prep -fo prepi
while execution I got the following error:
"Bond types are assigned for valence state 13 with penalty of 2"
What is the reason for this error?
As a result, I am although getting the prepi file but some of the oxygen
atoms were not coming in the resultant prepi and NEW.PDB files generated
by antechamber.
Please explain me the reason for this unusual behaviour.
I am having a Nitrate anion and another cation in my input system and the
oxygens of Nitrate are not coming.
THanks & Regards
Gurpreet
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Received on Sun Jan 13 2008 - 06:07:15 PST
