Re: creating topology for a unique structure

From: soroush ziaei (soroush.ziaei7337_at_gmail.com)
Date: Thu Nov 08 2018 - 14:29:17 CST

i'm willing to set 1,-1&0 in fep file according to tutorial.
what do you think?

On Thu, Nov 8, 2018 at 7:26 PM Brian Radak <brian.radak_at_gmail.com> wrote:

> 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 <soroush.ziaei7337_at_gmail.com>
> wrote:
>
>> 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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