AMBER Archive (2005)

Subject: Re: AMBER: Free energy pertubation (thermodynamic intergration)

From: Sichun Yang (syang_at_physics.ucsd.edu)
Date: Mon Apr 25 2005 - 11:55:16 CDT

I have a similar question, too.

My guess is that you can do it backwards and it might make the life
easier.

However, for my case, it doesn't solve my problem because I need to
change from Tyr to Pro -- I don't know how danger it is to do this kind of
TI. Any comments are welcome.

Thanks,
-Sichun

>
> I am using AMBER 8 and trying to preform some FEP calculation on guanosine
> triphosphate and its analogs. I'm not sure however to make atoms appear.
> What I am specifically trying to do is change a (H) into an (NH2). I was
> guessing that I might have to make some dummy atoms, but I am not sure the
> proper way to do this. Any help is greatly appreciated.
>
> Matthew Broadus
>
> ------------------------------------------------------------
> Illinois State University Webmail https://webmail2.ilstu.edu
>
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