[AMBER] WHAM-2D analysis

From: Alessandra Lacetera <alessandra.lacetera.gmail.com>
Date: Wed, 13 Jul 2016 18:55:20 +0200

I have performed an umbrella sampling to study a reaction in which there is
a formation of an OH (O from a glutamate and the H from a water molecule,
reaction 1) and then the nucleophilic attack of the hydroxide to a
phosphate group (reaction 2). So first I run a script for the first
reaction coordinate scan, using a step of 0.2 A and a force constant of 100
kcal/mol defining in this way the reaction coordinate:

rc_iat="iat=44916, 44918, 44918, 1527, rstwt=1,-1"

And with these keywords

&wt type='DUMPFREQ', istep1=1 /
&wt type='END' /

I had this output file (for e.g. rc0.0_1.tra)

       0 -0.355 3.617
       1 -0.255 3.620
       2 -0.119 3.623
       3 -0.003 3.628

The second reaction coordinate scan was performed fixing the first reaction
coordinate, using a step of 0.2 A and a force constant of 100 kcal/mol

iat=44916,44918, 44918, 1527, rstwt=1,-1

The output file was like:

       0 1.719 -2.359
       1 1.723 -2.362
       2 1.726 -2.369
       3 1.728 -2.381

It is not clear to me how to use wham-2D for crossing all the results for
generating the PMF and how to write a proper metadata file. In the tutorial
http://ambermd.org/tutorials/advanced/tutorial17/section3.htm, wham is
used, but not wham-2d and I was wondering if the metadata should be
different. Could you help me or point me to any tutorial about how to
generate the PMF?

Thank you in advance

Alessandra Lacetera
PhD Student CIB (CSIC)
Calle Ramiro de Maetzu, 9
28040, Madrid - Spain
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Received on Wed Jul 13 2016 - 10:00:03 PDT
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