Re: QSAR - DRAGON 3.0 - Can not process structures

Hi Jim,
After looking at the atom types on the phosphate groups, I would guess
that DRAGON is complaining about the atom types. As picky as it might
seem, you may have to change atom types on the P to O.3 and O.2 rather
than O.co2

regards,
Greg
----------------
Greg Durst
Computational chemistry
Eli Lilly & Co.
Indianapolis, IN USA

james.metz^^^abbott.com
Sent by: qsar_society-admin]-[accelrys.com
07/07/2003 02:07 PM
Please respond to qsar_society

 
        To: qsar_society++accelrys.com
        cc: james.metz[A]abbott.com
        Subject: QSAR - DRAGON 3.0 - Can not process structures

QSAR Society Colleagues,

        I am attempting to calculate molecular descriptors for the two
attached, non-proprietary molecules in SYBYL mol2
format using DRAGON 3.0 (1fbc.ml2 and 1fbf.ml2).

        The calculations fail with an error message "Hydrogens are
probably lacking." Since the molecules do contain
hydrogens, I am stumped trying to figure out what is the problem. I have
tried removing hydrogens and adding them back
on in SYBYL, but this does not help.

        If I repeat the calculations using DRAGON 2.1, the calculations
work fine.

        Perhaps someone thinks that DRAGON has problems processing
phosphate groups ? This apparently is NOT the
case. I have attached a third SYBYL mol2 file, 1csc_1.ml2, which works
just fine with DRAGON 3.0.

        I would be most grateful to anyone who has an idea what is going
on here !!! I am pulling my hair out on this one.

        Thank you,
        Jim Metz

James T. Metz, Ph.D.
Research Investigator Chemist

GPRD R46Y AP10-2
Abbott Laboratories
100 Abbott Park Road
Abbott Park, IL 60064-6100
U.S.A.

Office (847) 936 - 0441
FAX (847) 935 - 0548

james.metz(0)abbott.com