Re: [AMBER] Query regarding atom type using xleap

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Thu, 17 Feb 2011 00:11:29 -0800

Atom *names* are what appear in pdb files. As long as they are
unique within a residue that aspect is ok. They must also
agree with the atom names in the template file (prep or mol).
Atom *types* are assigned to the atom names in the template file,
are not necessarily unique within a residue, and must agree
with the force field definitions given in the ff papers.

Bill

----
I tried to prepare my ligand (extracted from a pdb) using XLEAP module. I
corrected the bond order and added the hydrogen. After saving the file in
pdb format gives me some atomtype followed *by asterisk (*)*. The pdb seems
ok when I visualize it in PYMOL.
Before moving to next step of preparing and inserting it into the protein
complex, I want to just confirm that there is nothing wrong with this atom
type.
*ATOM      1  C5* HAK     1       8.652   1.367  93.970  1.00  0.00
ATOM      2  O5* HAK     1       7.418   1.157  94.648  1.00  0.00
ATOM      3  C4* HAK     1       8.386   1.353  92.509  1.00  0.00
ATOM      4  N4* HAK     1       7.444   2.356  92.140  1.00  0.00
ATOM      5  C3* HAK     1       9.640   1.600  91.726  1.00  0.00
ATOM      6  O3* HAK     1       9.581   0.713  90.602  1.00  0.00
ATOM      7  C2* HAK     1       9.516   3.041  91.348  1.00  0.00
ATOM      8  O2* HAK     1       9.998   3.254  90.016  1.00  0.00
ATOM      9  C1* HAK     1       8.036   3.455  91.463  1.00  0.00*
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Received on Thu Feb 17 2011 - 00:30:02 PST