Dr. Case,
Thank you for the quick sanity check. Indeed, I read a wrong error message from one on the earlier runs
when I was testing Arzoxi vs Arzoxi-HCl and called the HCl varint without the -nc 1 flag. The error then
says it's an odd number of electrons and sends you to check the charge and multiplicity flags (once the -nc is
set correctly to 1, then m=1 or 2 yields the same results).
HOWEVER, the difference in the calculated partial charges by the two calls to antechamber (stand alone
and Chimera-style, both recognizing an EVEN number of electrons) remains, and I 'd like to clarify
which is the correct or better way to go:
antechamber -i LIG.pdb -fi pdb -o LIG-A14ante-bcc.mol2 -fi mol2 -nc 1 (stand alone)
antechamber -ek qm_theory='AM1', -i LIG.mol2 -fi mol2 -o LIG-ante.mol2 -fo mol2 -c bcc -nc 1 -j 5 (Chimera)
Best regards, Voytek Kasprzak
Wojciech (Voytek) Kasprzak (Contractor)
Analyst Programmer
Frederick National Laboratory for Cancer Research
Leidos Biomedical Research, Inc.
Post Office Box B
Frederick, Maryland 21702
Phone: 301-846-5537
kasprzaw.mail.nih.gov
http://binkley2.ncifcrf.gov/users/kasprzak
________________________________________
From: David A Case [david.case.rutgers.edu]
Sent: Wednesday, October 25, 2017 10:35 PM
To: AMBER Mailing List
Subject: Re: [AMBER] RNA with ligand - a follow-up ANTECHAMBER question
On Wed, Oct 25, 2017, Kasprzak, Wojciech (NIH/NCI) [C] wrote:
>
>
> The ligand is positively charged (+1), and the (Amber 14) antechamber call I used was as follows:
>
> > antechamber -i LIG.pdb -fi pdb -o LIG-A14ante-bcc.mol2 -fi mol2 -nc 1 -m 2 -s 2
I don't know what you ligand really is, but you should check that it really
has an odd number of electrons. The antehcamber scheme will only work for
closed-shell molecules. If you really have a stable radical, constructing
a force field for it will almost certainly involve a lot of hand-work. But
Arzoxifene itself has an even number of electrons, and *very* few organic
drug-like molecules are radicals.
>
> Chimera GUI, on the other hand, issues the following command:
> > antechamber -ek qm_theory='AM1', -i LIG.mol2 -fi mol2 -o LIG-ante.mol2
> > -fo mol2 -c bcc -nc 1 -j 5 -s 2
>
> Thus the multiplicity of 1 is assumed (default) and -j 5 - atom and part
> bond type.
Something odd is going on here, if the same +1 charge can yield structures
with both even and odd numbers of electrons. I don't think anyone on the list
will be able to resolve this without more information.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 26 2017 - 08:30:02 PDT
