On Thu, Jul 06, 2017, Bharat Manna wrote:
>
> I am trying to perform a SMD Simulation of a protein with different Ionic
> salts in NAMD. Some of the ff parameters are only found in the AMBER. So, I
> want to use the AMBER ff.
There are two links called "Using the Amber force field in NAMD" at
http://ambermd.org. One is provided by the UIUC folks and one come from
Rutgers.
> But, for SMD in NAMD I need to provide the force pulling direction (X , Y
> and Z) between the two specified atoms.
> SMDDir x y z
> Can anyone help me to figure out these direction form AMBER toplogy and
> inpcrd files?
I don't see how the direction of pulling has anything to do with force field
you are using. There is nothing in the Amber topology or coordinate files
that would help: you need to figure out the direction based on the particular
system you have.
...good luck...dac
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Received on Thu Jul 06 2017 - 05:00:02 PDT
