Re: [AMBER] Extending constant pH to additional titratable groups

From: Jason Swails <>
Date: Mon, 3 Jan 2022 12:12:30 -0500

How did you add the FMN definition to (specifically,
what are the *exact* changes you made to that file)? The cpinutil script
either was told not to make FMN titratable (either through some kind of
filter, like a min or max reference pKa), the FMN residue wasn't added to
the list properly (the updated file wasn't staged to
the right directory or there's another ParmEd installation conflicting with
the version you updated), or it didn't find a matching FMN residue in the
topology file.

With just the given information it's impossible to tell what went wrong,
and unfortunately this issue is going to be very challenging to remotely
diagnose without understanding most of the details about how Python and both work.


On Sun, Dec 26, 2021 at 9:45 AM 王金玉 <> wrote:

> Dear Amber Community,
> I want to parametrize a non-standard residue as titratable ones in
> Amber16, so I need to add the definition of FMN in,
> however, I have initially added the definition and recompiled amber, why
> does the cpin file generated with have no information about
> FMN? The cpin file and some information of definition has been uploaded to
> the attachment. Could you please help me point out the problem?
> Respects
> Wangjy
> _______________________________________________
> AMBER mailing list

Jason M. Swails
AMBER mailing list
Received on Mon Jan 03 2022 - 09:30:02 PST
Custom Search