Hi amberers,
I am trying to obtain new dihedral parameters, I performed PES scan
already. Now, I should obtain dihedral parameters with sander.I found a way
but I am not sure, so maybe you help me:
In this tutorial:
http://ambermd.org/tutorials/advanced/tutorial26/section2.html
dist.example.RST file looks like this:
&rst
iat=9,99,
r2=13,
r2a=17,
rk2=7.2,
&end
This is for bond distances according to tutorial. SO I thought and I
decided I can use this file to calculate dihedral energy with some edits.
Bu I am not sure how to use it dihedral. Is it okey if I use this file for
example 360 degree:
&rst iat= 1, 2 , 3 ,4
r1=360.00000, r2=360.000000, r3=360.000000, r4=360.000000, rk2=5000.0,
rk3=5000.0, /
and for 350 degree:
&rst iat= 1, 2 , 3 ,4
r1=350.00000, r2=350.000000, r3=350.000000, r4=350.000000, rk2=5000.0,
rk3=5000.0, /
and for 340 degree
&rst iat= 1, 2 , 3 ,4
r1=340.00000, r2=340.000000, r3=340.000000, r4=340.000000, rk2=5000.0,
rk3=5000.0, /
and so on......?
I am planning to obtain MM chart for my 1-2-3-4 dihedral with this way.
(After this,I will apply Genetic Algorithm to fit amber force field with QM
calculation) Am I doing right?
Thank you soo much by now.
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Received on Fri May 03 2019 - 03:00:02 PDT
