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

From: zoran matovic <>
Date: Fri, 8 Jul 2016 20:20:04 +0200

Are u sure you choose amber coordinates with periodic box in VMD (it is VMD
isn't it?). Something similar happens when one omit to select coord. with
period. box. Or, if everything is loaded into vmd properly, something with
FF parameters of your complex is very wrong, or you missed something to
write (or wrote incorrect) in the simulation input file.. You should also
check the parameters carefully once again and might be desirable to run
dynamics for the complex only just to be sure that things with complex are
going well.


-----Original Message-----
From: Saman Yousuf ali
Sent: Friday, July 8, 2016 7:48 PM
Subject: [AMBER] ligand bond distortion during MD run.

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,

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Received on Fri Jul 08 2016 - 11:30:03 PDT
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