[AMBER] problem with extra-point

From: Emilio Angelina <emilioluisangelina.hotmail.com>
Date: Sat, 25 Oct 2014 16:38:55 +0000

Hi all (and specially those having experience working with extra-points)

I am trying to add an extra-point (EP) at the tip of a Bromine atom to simulate the sigma-hole I used the same parameters to define the EP as Ibrahim (J Phys Chem B. 2012, 116:3659-69. doi: 10.1021/jp3003905). Attached is the frcmod file (extra-point.frcmod).
When I attempt minimizing the system (i.e. brominated ligand in the binding pocket of the receptor, attached is a pdb with the input coordinates) using sander or pmemd it exits with a segmentation fault error after 400 steps. I am also attaching the log file (D2h_haloBr_min.out). I can see really high values of GMAX that comes from EP and Br at the end of the run and also very high values of VDWAALS = 25549.7670 and EEL = *************.
When I look into the output coordinate file I can see that the EP has collpapsed into Bromine (i.e. both have the same coordinates).
I will really appreciate if someone can give me a hand with this issue.
Thanks in advance


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Received on Sat Oct 25 2014 - 10:00:01 PDT
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