AMBER Archive (2004)

Subject: Re: AMBER: antechamber gives GDP 0 charge

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Wed May 05 2004 - 15:46:06 CDT

Hi Raik,

> antechamber -i GDP_in.pdb -fi pdb -o GDP.prep -fo prepi -nc -3 -rn
GDP -at
> amber -c resp

you need to calculate the electrostatic potential of your molecule with
a QM program like gaussian if you want to apply the resp charge fit (-c
resp). Without the potential information no charges can be fitted.

If you want to go from the pdb structure directly to charges you can use
the AM1-BCC method (-c bcc).

Schoene Gruesse,
Oliver

Raik Grünberg wrote:
> Hi there,
>
> I just tried to create parameters for GDP and GTP using antechamber (Amber 7).
> Everything sort of worked but antechamber seemed to not only ignore the
> "-nc -3" parameter but actually assigned charge 0.0 to all atoms.
> It's the first time that I am using it, perhaps I made some obvious mistake.
> Here is the command:
>
>
> GDP_in.pdb was prepared from the X-ray structure. I deleted the addidtional P,
> added hydrogens in tleap and added back the P.
>
> parmchk -i GDP.prep -f prepi -o frcmod.gdp
> gives a frcmod in which some bond angles are marked as missing, although they
> are existing in the parm99.dat. I just copied them over from parm99.dat.
>
> tleap loads the prep and then the PDB without trouble but all the atoms have 0
> charge. Any ideas anyone, what could have gone wrong?
>
> Or alternatively, has anyone already parameters ready for GDP / GTP?
>
> Many thanks!
> Raik
>
> -----------------------------------------------------
> Raik Grünberg | Bioinformatique Structurale
> | Institut Pasteur
> Tel: +33/1.45.68.87.37 | Paris, France
> -----------------------------------------------------
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-- 
_______________________________________________________________

Oliver Hucke, Dr.
                               Health Sciences Building - K418C
University of Washington      1959 NE Pacific St.
Dept. of Biochemistry         phone: (206) 685 7046
Box 357742                    fax  : (206) 685 7002
Seattle, WA 98195-7742        email: ohucke_at_u.washington.edu
_______________________________________________________________

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