Hello,
Sikander,
There is no info available regarding force field parameters for the Ca and phosphate in ff03 force field. You need parameters for these two. Most probably you can find papers regarding bonded or non-bonded parameters for Ca2+ and bonded parameters for phosphate anion.
Another way to make a library for the calcium ion with the atom types as specified in the parm.dat file.
Regards
--- On Tue, 2/16/10, sikander azam <syedazam2008.gmail.com> wrote:
From: sikander azam <syedazam2008.gmail.com>
Subject: [AMBER] Calcium and Phosphate
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Tuesday, February 16, 2010, 10:12 PM
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.
PS: Sorry if I am writing this email twice.
Best
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Received on Wed Feb 17 2010 - 02:30:07 PST
