Re: creating topology for a unique structure

From: Brian Radak (
Date: Thu Nov 08 2018 - 09:55:53 CST

Unfortunately, running alchemical calculations within non-standard
mutations (e.g. those not supported by the mutator plugin) does require
manual creation of a new residue and/or residue patch. There is no way
around this at present and the only official guidance is to follow the
example from the tutorial. For this reason alchemical calculations are
generally considered an advanced feature.

What number are you referring to? I'm inclined to say "no", you probably
should not set something to an arbitrary number.

On Wed, Nov 7, 2018 at 3:36 PM soroush ziaei <>

> thanks for your reply, dear brian.
> i must to tell you, i have read topology & fep tutorial but the examples
> of fep & topology tutorial file have been exist in < top_all22_prot.inp >.
> and i'm not able to build a unique topology for some structure according
> to general topology...
> can i set this number in fep file arbitrary?
> regards,
> soroush

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