AMBER Archive (2002)

Subject: Re: Protonate doesn-t recognize by pdb input file

From: Stéphane Teletchéa (steletch_at_biomedicale.univ-paris5.fr)
Date: Thu May 23 2002 - 07:23:31 CDT

Le Mercredi 22 Mai 2002 18:20, David Case a écrit :
> Stéphane Teletchéa wrote that protonate was failing to add hydrogens
> to thymine. (Sorry, but I have lost the original message).
>
> First, there is a bug [the second long-dormant bug to have been found
> so far today :-( ] See bugfix.13 for Amber 7 on the amber web site.
> You can also apply this patch by hand (it's a one-line fix) to amber6
> source code as well.

Thanks. Problem solved now.

> Second, Stef's pdb files were missing the C7 atom for thymine. This could
> cause problems down the line -- protonate certainly won't add the methyl
> protons if there is no methyl carbon.

I saw that, but it is coming from discrepancies between naming conventions in
certain PDB : sometimes the name is C7, sometimes C5M (and so is for the
protons names 1H7 or 1C5M).

> Third, Stef said:
>
> "I intended to use this in a script, so I don't want to use xleap for that"
>
> I'll just note that tleap is fine for scripts, and I think is really what
> most experienced amber people use more than xleap.

I'm sure i can trust you, but as protonate was recommended in AMBER6's
tutorial, in this particular situation ...

> ...thanks for the problem report...hope the above helps....dac

Thanks for the quick reply.

Stef