[gmx-users] ligand topology

Justin Lemkul jalemkul at vt.edu
Thu Jan 31 17:03:11 CET 2013

On 1/31/13 9:51 AM, az kalsom wrote:
> hi
> i have docked the compund with protein and selected the best protein-ligand
> conformation for simulations,
> but when i generate the topolgy for ligand by
> Automated Topology Builder (ATB) and Repository , job is killed every tym.
> error message is 1) geometry was inappropriate; (2) the number of hydrogen
> atoms or the net charge was inappropriate...
> what should i do to remove this ?

There's clearly something wrong with your input, but since (1) we don't know 
what it is, (2) we don't know what you're doing, and (3) this forum isn't about 
ATB, it's pretty hard to help.

Refer to the FAQ (http://compbio.biosci.uq.edu.au/atb/index.py?tab=faq_tab) and 
seek help from whatever resources ATB provides.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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