AMBER Archive (2009)

Subject: [AMBER] charge derivation for ATP molecule using antechamber

From: prachi munjal (prachimunjal14_at_gmail.com)
Date: Fri Jan 23 2009 - 07:19:27 CST

Hello Sir

I downloaded "mol2" file of ATP molecule from ChemDB but there is no charge
added to the molecule.
As the total charge on ATP always be -4 because of four phosphate oxygens
each with -1 charge. So, there should not be any hydrogen added to those
four oxygens.
Hence, I deleted those four hydrogens & ran the following antechamber
command on that molecule ( Also find the changed mol2 file as attachment)
for assigning -4 charge.

antechamber -i ATP_1.mol2 -fi mol2 -o ATP_1charges.mol2 -fo mol2 -c bcc -nc
-4.0

But its giving the following error :

*"Cannot successfully assign bond type for this molecule, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C"

*Can you please guide me in this respect.

With Regards
Prachi



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