Re: [AMBER] ligand bond distortion during MD run.

From: Daniel Roe <>
Date: Fri, 8 Jul 2016 14:12:26 -0600

It could be a lot of things. How did you generate your ligand
parameters, or where did you obtain them from? What were your input
settings for your production run? How much equilibration did you do
prior to your production run? You'll have to provide more information
and details on exactly what you are doing - otherwise all anyone can
do is guess.


On Fri, Jul 8, 2016 at 11:48 AM, Saman Yousuf ali
<> wrote:
> Dear all,
> What are the possible reasons for ligand structure distortion (bonds stretching during production run? How we can avoid this problem. Picture of ligand distortion during MD is attached below. Thanks in advance. Regards, Sarah
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Jul 08 2016 - 13:30:03 PDT
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