[AMBER] Problem of calculating the Van der Waals energy between two proteins

From: Tan-MIng Chi <tmjonathanchi.gmail.com>
Date: Sat, 9 Nov 2013 11:33:14 +0800

Dear all,

I am the newcomer for using AMBER (version 11). I have read the reference
manual, mail list and some tutorial in website, but I still have no idea
how to do my purpose. The previous student have graduated for several
years, so I need to do this work by myself.

There is what I want to do:
I have two alpha helices (proteins) extracted from PDB, and I want to
calculate the Van der Waals energy between them.

1. I want to determine the distance between two center of mass of two
helices. It seem like need to use ptraj (distance), but I can't understand
the statement of manual.

2. How to separate the distance from above? (For example, if I want to set
distance = 5, which command can be used to determine or move them?)

3. I want to fix this distance, and let one of them can rotate or tilt
(just no translation). It seem like I could use
IRESID = 0, IAT(3) = 0. But I need a more specific example. For calculating
the Van der Waals energy, how should I do for "two proteins" simulation (MD
simulation?) ?

Noted that I have known how to do the energy minimization and basic
molecular dynamics of "one protein" (learning from tutorial), but I have no
idea for two proteins simulation.

I just want some of the direction (the example is better, but I know is too
unjustifiable) or any suggestion (like: see the AMBER 12 manual Chapter 4.1
or tutorial A2).
Thank you for reading.

Best Regards,
Jonathan Chi
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Received on Fri Nov 08 2013 - 20:00:02 PST
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