AMBER Archive (2009)

Subject: [AMBER] re: net charge

From: Vishal Maingi (
Date: Tue Jun 23 2009 - 13:56:52 CDT

dear amber users,

apology for incomplete information.

in antechamber (seems to be incorrect to me also) I used input mol2 file to make out mol2 file also.its here in this case net charge is -2 with error:

antechamber -i new.mol2 -fi mol2 -o main.mol2 -fo mol2 -c bcc
Total number of electrons: 284; net charge: -2
Running: /opt/amber10/bin/
Error: unable to find mopac charges in mopac.out

but in other case using mol2 input and output as pdb net charge is zero also two electrons are less (here I didnt use -nc flag):

antechamber -i new.mol2 -fi mol2 -o abc.pdb -fo pdb -c bcc
Total number of electrons: 282; net charge: 0
Running: /opt/amber10/bin/

coming to my query:

1) why in mol2 to mol2 conversion showing net charge -2 not zero

2) by using my minimised residues the molecule so generated in amber(new.mol2) shows charge perturbed and unperturbed to be nonzero negative value in xleap edit (UNIT----->net charge option). I saved my molecule in mol2 form(new.mol2). the residues so minimised are neutral and all hydrogen are there in molecule so built

 but the pdb file so generated by antechamber (abc.pdb) if edit in xleap shows net perturbed and unperturbed to be of zero value



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