When using constraints (SHAKE), Amber uses a special analytical constraint
algorithm (called SETTLE) to constrain water geometries (3-constraint
systems can be solved analytically). To recognize water residues to apply
SETTLE to, sander and pmemd use the residue and atom names to identify
them. The defaults are 'WAT', 'O', 'H1', and 'H2'. tleap *always* assigns
these names to water atoms and residues, so Amber users rarely have to
change them.
However, I think CHARMM uses different names for water residues (not sure
about atoms): TP3 (if using tip3p). So you have to override the "watnam"
variable in the input file to tell sander/pmemd how to find water residues.
In the &cntrl namelist, put watnam='TP3' (or whatever the water residue
name in your topology file is).
HTH,
Jason
On Wed, Feb 16, 2022 at 3:33 PM Artur Hermano <artur.hermano.hotmail.com>
wrote:
> Hello, Amber users!
>
> I am receiving the following error message when I try to minimize my
> system (protein+glycan+peptide in a water box):
>
> Error: Fast 3-point water residue, name and bond data incorrect!
>
> I have originally built my system using CHARMM ff, then converted it to
> Amber input files using Chamber through Parmed. I cannot imagine what
> water-related issue can be happening here, and the web results do not seem
> of great help either. Do you guys have any idea what might be wrong here or
> what I should examine more carefully?
>
> Thank you!
>
> Artur
>
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>
--
Jason M. Swails
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Received on Fri Feb 18 2022 - 07:30:03 PST
