AMBER Archive (2005)

Subject: AMBER: Cut pdb files

From: Yogesh Sabnis (ysabnis_at_yahoo.com)
Date: Thu Jun 16 2005 - 02:57:18 CDT

Hello,

I dock molecules not in a whole protein but in a cut
pdb file (around 10Å to enhance the speed of
calculations), I was wondering if the cut pdb files
canbe opened in Amber8.0

I dock molecules in QXP/FLO which uses compressed
macromodel file format. I subject the ligand to
multiple conversions and am able to create the .prep
and .parm files for the ligand. But when I try to load
the complex, the program crashes. I am attaching the
leap.log file.

I would appreciate if you could throw light on this
issue. Let me know if you need more indepth report.

Thank you

Kind regards,

Yogesh

########################

Yogesh Sabnis, PhD

BMC, Box 574,

Avd Org. Farm. Kemi,

Husargatan 3,

Uppsala - 751 23

Sweden

                
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