Hi
Please provide the structure of your molecule, otherwise it is very
difficult to figure out the problem.
Best
Junmei
On Thu, Oct 26, 2017 at 11:10 AM, Kasprzak, Wojciech (NIH/NCI) [C] <
wojciech.kasprzak.nih.gov> wrote:
> 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
>
>
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Received on Thu Oct 26 2017 - 09:00:01 PDT
