AMBER Archive (2009)

Subject: Re: [AMBER] atom numbers

From: Vikas Sharma (vs_vikassharma_at_yahoo.co.in)
Date: Tue Apr 21 2009 - 13:36:35 CDT

Dear Dr. David Case

i sent you attached files in my previous mail(the one before this)

..please check those...the toms are two C and $ oxygens..i tried to
name them but i dnt know which technique to follow...i checked the mol2
file in sybyl and there again it is showing the same thing...all the
atoms have unique names except C,O,O of the -COOH groups...all the
other atoms are named like H20,C1,C2...etc but the C,O,O of the two
_COOH groups are named as C,O,Oand C,O,O....

--- On Tue, 21/4/09, David A. Case <case_at_biomaps.rutgers.edu> wrote:

From: David A. Case <case_at_biomaps.rutgers.edu>
Subject: Re: [AMBER] atom numbers
To: "AMBER Mailing List" <amber_at_ambermd.org>
Date: Tuesday, 21 April, 2009, 10:56 PM

On Tue, Apr 21, 2009, Vikas Sharma wrote:

> i checked in my PDB and found out that indeed there are a few atom names
> which are same..

OK, then get a text editor out, and start fixing the PDB file.  Both the
residue name (maximum 3 characters) and the atom names (max four
characters) must match between the pdb file and the mol2 file.  Your
mol2 file was created by sybyl (apparently).  You will need to use
antechamber to convert this to a gaff-compliant mol2 file.

...dac

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