Yes Jason,
are clearly the waters the problem. It is fixed now.
thank you all for the help
Giulia
2016-08-25 10:34 GMT-07:00 Jason Swails <jason.swails.gmail.com>:
> On Thu, Aug 25, 2016 at 11:12 AM, giulia palermo <giulia.palermo83.gmail.com
>> 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.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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Received on Thu Aug 25 2016 - 16:00:02 PDT
