There is something wrong with your installation/implementation of AMBER Tools 19, because the "leaprc.water.tip3p" must load the Na+ residue from the library "atomic_ions.lib"... I tied to do it myself and it worked perfectly...
Indeed, the "atomic_ions.lib" is being loaded from your working directory (./) instead of the AMBER database, which in your case I guess is located at /home/ravi/anaconda3/dat/leap/lib, and it seems to only contain the ZN residue, that's rare...
Best,
Matias
----- Mensaje original -----
De: "shivangi agarwal" <shiviagarwalpharma.gmail.com>
Para: "David Case" <david.case.rutgers.edu>, "AMBER Mailing List" <amber.ambermd.org>
Enviados: Miércoles, 24 de Julio 2019 0:50:12
Asunto: Re: [AMBER] Error in preparing system using AmberTools19
I have attached the leap.log file.
I checked using list command
*com* is there
but as I am getting error during addition of Na+,
So Na+ is not there.
Kindly look into the leap.log file and suggest
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Received on Wed Jul 24 2019 - 12:00:02 PDT
