Hi Users,
I am having a protein with Ca and Phosphate. I came to know through search
that atom type for Calcium should be C0. In my pdb file it happens to be as
under:
HETATM 2809 C0 Ca2 A1356 4.902 31.422 21.076
HETATM 2810 C0 Ca2 A1357 9.862 26.279 23.131
HETATM 2811 P PO4 A1358 12.263 24.882 25.290
HETATM 2812 O1 PO4 A1358 10.821 25.112 24.781
HETATM 2813 O2 PO4 A1358 12.995 23.970 24.323
HETATM 2814 O3 PO4 A1358 12.237 24.170 26.585
HETATM 2815 O4 PO4 A1358 13.018 26.210 25.500
TER 2816 P04 A1358
END
While I am having following output loading in xleap
Loading PDB file: ./PON-15.pdb
Unknown residue: Ca2 number: 355 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: Ca2 number: 356 type: Nonterminal
Unknown residue: PO4 number: 357 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: Ca2 sequence: 356
Created a new atom named: C0 within residue: .R<Ca2 356>
Creating new UNIT for residue: Ca2 sequence: 357
Created a new atom named: C0 within residue: .R<Ca2 357>
Creating new UNIT for residue: PO4 sequence: 358
Created a new atom named: P within residue: .R<PO4 358>
Created a new atom named: O1 within residue: .R<PO4 358>
Created a new atom named: O2 within residue: .R<PO4 358>
Created a new atom named: O3 within residue: .R<PO4 358>
Created a new atom named: O4 within residue: .R<PO4 358>
total atoms in file: 2814
Leap added 2769 missing atoms according to residue templates:
2769 H / lone pairs
The file contained 7 atoms not in residue templates
Kindly suggest me to remove these errors as I am using AMBER 10 with ff03.
Best
On Thu, Feb 4, 2010 at 3:48 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> > While In the following directory
> >
> > /usr/local/amber11/exe
> >
> > I found xleap but it is not running and giving error
>
> This means you have xleap from AMBERTools 1.3 built. AMBERTools 1.3
> extracts
> into the directory AMBER 11.
>
> > Error: you must set the AMBERHOME environment variable!
>
> This is the error. You need to set this environment variable. It is only
> used by AMBERTools, not sander, pmemd etc so you would simply point this at
> AMBER11. e.g.
>
> for bash shell:
> export AMBERHOME=/usr/local/amber11/
>
> for csh shell:
> setenv AMBERHOME=/usr/local/amber11/
>
> Then xleap should run fine with AMBERHOME/exe/xleap (or by adding
> $AMBERHOME/exe/) to your path.
>
> You should probably add the AMBERHOME definition to your .bashrc or .cshrc
> file so it gets set everytime you login.
>
> Good luck,
> Ross
>
>
>
>
> _______________________________________________
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>
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Received on Tue Feb 16 2010 - 05:00:03 PST
