AMBER Archive (2005)

Subject: Re: AMBER: problem of calculate the charge

From: ping jiang (p_jiang2000_at_yahoo.com)
Date: Fri Dec 30 2005 - 12:48:41 CST

Thanks a lot!
Now it works. I think I made a mistake when I load the
file.
Except load "prepin & frcmod" files, I also "loadoff
UAL.lib", I think I should not load this libaray file.

For the "TER" card, I don't know why it generate it,
maybe because I build undecyl first, then I made the
seqence of undecyl-ala-leu, so the program think they
are two different molecules.
Regards,
Ping

--- "David A. Case" <case_at_scripps.edu> wrote:

> On Tue, Dec 27, 2005, ping jiang wrote:
> >
> > I am struggling with assigning the charge for the
> > atoms in the molecule.
> > Here I attached the PDB file for the
> undecyl-ala-Cleu
> > (charge: -1)molecule that I built.
> >
> > Then I use antechamber to generate the charge
> (AM1-bcc
> > method)by using:
> > $AMBERHOME/exe/antechamber -i UAL.pdb -fi pdb -o
> > UAL.prepin -fo prepi -c bcc -nc -1 -s 2
> >
> > If we checked the "edit selected atoms", you can
> see
> > the undecyl part, the atom charge is Zero.
>
> I cannot reproduce this problem. I used your input
> UAL.pdb file, and the
> charges look pretty reasonable to me (not zero on
> the cyl part, etc.).
>
> Can you just look at the UAL.prepin file itself to
> check the charges? Also,
> look at the divcon or mopac output file for any
> clues as to what might be
> going wrong. Are you getting reasonable charges on
> the peptide group? Which
> version of Amber/antechamber are you using?
>
> You might be having a problem because of the TER
> card inside the UAL.pdb file.
> TER cards should only be placed between separate
> molecules, although I think
> antechamber ignores this. Remember that antechamber
> really works on just
> whole molecules.
>
>
> ...dac
>
>
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