AMBER Archive (2006)
Subject: Re: AMBER: antechamber charge calculation very sensitive to conformations ?
From: David Mobley (dmobley_at_gmail.com)
Date: Fri Aug 25 2006 - 10:08:44 CDT
I had a look at these, too. It seems puzzling that in one case the
three hydrogens on the amide group in question have very different
charges. I had thought that AM1-BCC, like RESP, was supposed to
recognize symmetries like this. Am I mistaken?
On 8/24/06, Junmei Wang <jwang_at_encysive.com> wrote:
> Hi, Chris,
> AM1-BCC method does corrections (based on both atom types and bond
> types) on AM1 Mulliken charges. The difference between the two sets of
> charges was caused by the difference of the AM1 Mulliken charges of the
> two conformations. Please refer to the attached output of AM1
> optimization by mopac. It is said that AM1 Mulliken charges are not very
> sensitive to conformations (at least compared to RESP charges), and this
> feature is considered as one of the advantages of AM1-BCC method.
> However, for this particular case, the differences is very large. I am
> not clear what is the reason.
> All the best
> Dear Amber(l)ist ,
> I found that charges calculated with Antechamber/mopac (v1.25) on two
> very close ligand conformation (RMSD = 0.45A) could lead to some
> surprising different charges on Atoms.
> antechamber -nc 5 -rn lig -i liga_regul.pdb -fi pdb -o liga_regul.mol2
> -fo mol2 -c bcc -j 4 -at gaff -pf y
> antechamber -nc 5 -rn lig -i lig_mini.pdb -fi pdb -o lig_mini.mol2 -fo
> mol2 -c bcc -j 4 -at gaff -pf y
> Please find in the attachment the mol2 files "liga_regul.mol2" and
> "lig_mini.mol2" , H7 (from NH3+) has a charge of +0.05 in
> "liga_regul.mol2" where is it +0.48 in "lig_mini.mol2".
> Graphicaly looking to these conformations, I can't understand why H7
> charge is so different , and moreover its charge is different than the
> two other H in -NH3+ (HN51, HN52)
> It looks like it is structure dependent, if you start again from the
> previous mol2 files , you have the same result and charge different for
> H7. antechamber -nc 5 -rn lig -i liga_regul.mol2 -fi mol2 -o
> liga_regul_NEW.mol2 -fo mol2 -c bcc -j 4 -at gaff -pf y antechamber -nc
> 5 -rn lig -i lig_mini.mol2 -fi mol2 -o
> lig_mini_NEW.mol2 -fo mol2 -c bcc -j 4 -at gaff -pf y
> My question is the following:
> 1) It is normal to find such charges difference for a slightly
> ddifferent conformation ?? If so , I guess, it would be a good idea to
> first optimize (I thought MOPAC would do it) the conformation before
> calculating the charges with Antechamber.
> Thanks a lot for any thought.
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