Hi,
On Thu, 29 Mar 2007, David A. Case wrote:
> On Thu, Mar 29, 2007, Scott Brozell wrote:
> >
> > Why does antechamber not obey the pdb format ?
> > http://www.wwpdb.org/documentation/format23/sect9.html
> > For example, it puts the atom name into column 17; see below.
>
> Patches are welcome. You should always cc complaints about antechamber
> to Junmei (jwang.encysive.com), since I don't think Junmei reads the actual
> lists.
ok, btw I just committed several other antechamber
bug fixes and improvements.
> Also, since (in principle) antechamber is being merged into gleap, so we may
> eventually have *one* pdb-writing routine, and hence only one place to fix
> problems like this.
fantastic; do we have a schedule (from which to fall behind :)?
> But for now, just fix up the antechamber source code. We also probably need
> to think about adding a REM card giving the pdb format, since pdbformat 2.3
> differs from format 3 in this regard.
According to
http://www.wwpdb.org/documentation/format30/sect9.html
"The character/column format of the ATOM/HETATM records is not changed."
So I may be misreading something.
Nevertheless, a REM card with pdb version and other info is a great idea.
> > Why does antechamber alter atom names ?
> > When will there be an option to prevent name mangling ?
>
> Examples? Where does antechamber alter atom names?
>From my original email:
HETATM 2176 1HH3 ACT A 69 35.916 18.297 8.799 1.00 0.00 H
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM 3 HH31ACT 69 35.916 18.297 8.799
1HH3 has become HH31 or HH3 depending on the pdb reader.
Scott
Received on Sun Apr 01 2007 - 06:07:32 PDT
