AMBER Archive (2004)

Subject: Re: AMBER: antechamber

From: Xin Hu (hux_at_mail.rockefeller.edu)
Date: Thu Jul 15 2004 - 15:57:09 CDT

>
> > >antechamber -i Ligand.pdb -fi pdb -o Ligand.prep -fo prepi -c bcc
> > >parmchk -i Ligand.prep -f prepi -o Ligand.parm
> >
> > In xleap:
> > >source leaprc.ff99
> > >source leaprc.gaff
> > >loadamberprep Ligand.prep
> > >loadamberparams Ligand.parm
> >
> > and then load the protein/ligand complex, save the paramter
> > files for MD
> >
> > >M=loadpdb protein.ligand.pdb
> > >saveamberparm M M.top M.crd
> >
> > Is there a better way to do that?
> > Thank you for your suggestion.
>
> Not really. Ideally such a thing should be too automated as that makes
> mistakes much harder to spot. However, if you wanted to automate this you
> could always use tleap and have it source a command file. If you load xleap
> and go through the stages you want exactly you will get a leap.log file.
> This you can then source using tleap with tleap -s leap.log and it will
> carry out the same commands you did. In this way you can put all of the
> commands into a single shell script that you can run from the command line.
> Thus if you had say a 100 different ligands to create prmtop files for you
> could write a script that creates a file containing the leap commands you
> want, run antechamber and then tleap and then writes the commands for the
> next ligand etc etc.
>

Hi Ross,

Thank you for your suggestions. I will try to see how it works on a number of ligands automatically using script.

Generally I just use this procedure to deal with a single protein/lgiand complex, as I donot know how other people process their protein/ligand

complexes in general, I woner if there is a better way, or alternative way, to do that?

I have another question, for a protein comlexed with ATP, the xleap can't recognize the ATP, do I need to process the ATP as an usual molecule using antechamber?

Thank you for your help.

Xin

The pdb file of ATP extracted from protein complex like that:

HETATM 1 PG ATP 1 1.061 23.237 30.731 1.00 0.00
HETATM 2 O3B ATP 1 0.509 21.824 31.117 1.00 0.00
HETATM 3 PB ATP 1 1.505 20.908 30.318 1.00 0.00
HETATM 4 O3A ATP 1 0.681 19.592 30.624 1.00 0.00
HETATM 5 PA ATP 1 1.566 18.372 30.138 1.00 0.00
HETATM 6 O5' ATP 1 0.497 17.155 30.218 1.00 0.00
HETATM 7 C5' ATP 1 0.000 16.321 29.145 1.00 0.00
HETATM 8 C4' ATP 1 -0.920 15.087 29.502 1.00 0.00
HETATM 9 C3' ATP 1 -1.960 15.285 30.651 1.00 0.00
HETATM 10 O3' ATP 1 -3.266 14.728 30.305 1.00 0.00
HETATM 11 H ATP 1 -3.728 15.275 29.678 1.00 0.00
HETATM 12 H4 ATP 1 -2.042 16.339 30.970 1.00 0.00
HETATM 13 C2' ATP 1 -1.411 14.388 31.789 1.00 0.00
HETATM 14 O2' ATP 1 -2.425 13.998 32.774 1.00 0.00
HETATM 15 H ATP 1 -2.652 14.775 33.281 1.00 0.00
HETATM 16 H5 ATP 1 -0.565 14.916 32.263 1.00 0.00
HETATM 17 C1' ATP 1 -0.852 13.229 30.921 1.00 0.00
HETATM 18 N9 ATP 1 0.110 12.326 31.630 1.00 0.00
HETATM 19 C4 ATP 1 0.092 10.979 31.631 1.00 0.00
HETATM 20 N3 ATP 1 -0.779 10.109 31.076 1.00 0.00
HETATM 21 C2 ATP 1 -0.539 8.786 31.221 1.00 0.00
HETATM 22 H8 ATP 1 -1.217 8.061 30.784 1.00 0.00
HETATM 23 N1 ATP 1 0.543 8.344 31.897 1.00 0.00
HETATM 24 C6 ATP 1 1.407 9.201 32.489 1.00 0.00
HETATM 25 N6 ATP 1 2.437 8.698 33.201 1.00 0.00
HETATM 26 H ATP 1 2.535 7.684 33.349 1.00 0.00
HETATM 27 H9 ATP 1 3.065 9.342 33.709 1.00 0.00
HETATM 28 C5 ATP 1 1.222 10.586 32.332 1.00 0.00
HETATM 29 N7 ATP 1 1.907 11.702 32.677 1.00 0.00
HETATM 30 C8 ATP 1 1.203 12.774 32.275 1.00 0.00
HETATM 31 H7 ATP 1 1.487 13.803 32.444 1.00 0.00
HETATM 32 H6 ATP 1 -1.655 12.619 30.485 1.00 0.00
HETATM 33 O4' ATP 1 -0.158 13.903 29.852 1.00 0.00
HETATM 34 H3 ATP 1 -1.487 14.797 28.597 1.00 0.00
HETATM 35 H1 ATP 1 0.851 15.902 28.584 1.00 0.00
HETATM 36 H2 ATP 1 -0.565 16.981 28.469 1.00 0.00
HETATM 37 O2A ATP 1 2.583 17.638 30.961 1.00 0.00
HETATM 38 O1A ATP 1 2.139 18.246 28.764 1.00 0.00
HETATM 39 O2B ATP 1 2.759 20.533 31.015 1.00 0.00
HETATM 40 O1B ATP 1 1.540 20.940 28.828 1.00 0.00
HETATM 41 O3G ATP 1 2.513 23.519 30.625 1.00 0.00
HETATM 42 O2G ATP 1 0.660 24.013 31.941 1.00 0.00
HETATM 43 O1G ATP 1 0.224 23.930 29.715 1.00 0.00

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