Dear Alex,
Leap doesn't call PACKMOL to create the solvent box, you have to use it independently from command-line...
Additionally, the "solvate.in" 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 [
http://ambermd.org/doc12/Amber20.pdf]
Best regards,
Matías Machado
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "库米尔" <418025.mail.dhu.edu.cn>
Para: amber.ambermd.org
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.
solvate.in
# 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
leapin leap.solvate.in
# Tolerance (# of waters off from target allowed)
tol 3
# 1 - Solvatebox
mode 1
solventunit TIP3PBOX
and
leap.solvate.in
source leaprc.water.tip3p
set default pbradii mbondi2
using the following command tleap -s -f solvate.in
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
Thanks
Alex
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Received on Sun Mar 21 2021 - 08:30:02 PDT
