Re: [AMBER] problem upon optimization

From: Jason Swails <>
Date: Thu, 25 Aug 2016 13:34:44 -0400

On Thu, Aug 25, 2016 at 11:12 AM, giulia palermo <
> wrote:

> Dear all,
> Amber is giving the following error, when running in NVT upon optimization:
> default_name
> begin time read from input coords = 0.000 ps
> Number of triangulated 3-point waters found: 57564
> can you give me some insights?
> The water named 57564 has no problem.
> In the system, I have named some water molecules as WAX (because I
> want to distinguish the crystallized ones), but the Force Field is the
> same of WAT (TIP3P).

​Don't rename waters. Amber uses residue and atom names to identify water
residues to treat using SETTLE (an analytical solution to 3 constraints
used to improve simulation of water).

You can use residue indexes to distinguish xtallographic waters from waters
that were added, since those don't change throughout the simulation (and
tleap should put additional waters *after* crystallographic ones).

Also keep in mind that exchange can and most likely will happen, meaning
that the labels won't correspond to the water molecules at the
xtallographic sites after some amount of time.


Jason M. Swails
AMBER mailing list
Received on Thu Aug 25 2016 - 11:00:03 PDT
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