Re: [AMBER] Solvating my box with specified number of water molecules

From: Matias Machado <>
Date: Sun, 21 Mar 2021 12:08:00 -0300 (UYT)

Dear Alex,

Leap doesn't call PACKMOL to create the solvent box, you have to use it independently from command-line...

Additionally, the "" file is not properly formatted for leap... none of the following keywords/commands are valid: target, buffer, pdb, top, leapin, tol, mode...

Please, take a time to read the AMBER Tools 20 Reference Manual []

Best regards,

Matías Machado

Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "库米尔" <>
Enviados: Sábado, 20 de Marzo 2021 13:20:21
Asunto: [AMBER] Solvating my box with specified number of water molecules

Dear Amber,
I want to solvate my molecules packed into a box using packmol with specific number of water molecules 4752 with the following scripts I found.
# Target number of waters
target 4752
# Initial guess for buffer
buffer 10
# Input PDB name
pdb sys.pdb
# Output topology name
top ionicbox.prmtop
# Output coordinates name
crd ionicbox.rst7
# Base leap input script
# Tolerance (# of waters off from target allowed)
tol 3
# 1 - Solvatebox
mode 1
solventunit TIP3PBOX

source leaprc.water.tip3p
set default pbradii mbondi2

using the following command tleap -s -f

But I always get this error

/home/lexis10k/Desktop/Amberpackage/amber20/bin/teLeap: Fatal Error!
Error from the parser: syntax error
Please kindly help me identify where the syntax error is. Am new to scripting



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Received on Sun Mar 21 2021 - 08:30:02 PDT
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