[AMBER] minimization problem

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From: Emilio Angelina <emilioluisangelina.hotmail.com>
Date: Thu, 13 Nov 2014 20:52:28 +0000

Hi all,

I am running a minimization of a haloperidol-like compound in a cubic box o waters. After a small number o minimization cycles, the ligand breaks into several parts. I guess that the problem might be in the definition of bonds/angles/dihedrals in the topology file. However, it is hard for me to find where exactly is the problem.
I am attaching the ligand before and after the minimization and also the topology (without waters) and frcmod files.
I will appreciate any suggestion or help.

Emilio

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chemical/x-pdb attachment: halo-Br-noEP_min.pdb

chemical/x-pdb attachment: halo-Br-noEP.pdb

application/octet-stream attachment: halo-Br-noEP.prmtop

application/octet-stream attachment: halo-Br-noEP2.frcmod

Received on Thu Nov 13 2014 - 13:00:02 PST