Re: [AMBER] Error in preparing system using AmberTools19

From: Matias Machado <>
Date: Wed, 24 Jul 2019 16:21:35 -0300 (UYT)

After digging deeper into your "leap.log" I may found the problem...

> i = createAtom ZN Zn2+ 2.0
> set i element "Zn"
> set i position { 0 0 0 }
> r = createResidue ZN
> add r i
> ZN = createUnit ZN
> add ZN r
> saveOff ZN ./atomic_ions.lib
Saving ZN.

So it seem you've been doing a lot of custom "trial and error" stuff...

Hence I recommend you to remove the leap.log file (because it's very messy) and start from scratch with you system setup...

First load the parameter in the proper way (e.i. by using the cmd files), then load the coordinates and at last add solvent and ions...

# Example after decoding your log file:

# Load parameters
source leaprc.protein.f14SB
source leaprc.water.tip3p
source leaprc.gaff

# Load coordinate
com=loadpdb complex_42_final_2_noH.pdb

# Solvate and add ions
solvateBox com TIP3PBOX 10.0
addIonsRand com Na+ 0

# Save topology and coordinates in netcdf
saveAmberParmNetcdf com XXX.prmtop XXX.ncrst



PS: this is a guess, I don't know what's in you system, so there may be missing parameters to check...

----- Mensaje original -----
De: "Matias Machado" <>
Para: "AMBER Mailing List" <>
CC: "David Case" <>
Enviados: MiƩrcoles, 24 de Julio 2019 15:58:53
Asunto: Re: [AMBER] Error in preparing system using AmberTools19

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...



----- Mensaje original -----
De: "shivangi agarwal" <>
Para: "David Case" <>, "AMBER Mailing List" <>
Enviados: MiƩrcoles, 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 - 12:30:02 PDT
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