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

From: 库米尔 <418025.mail.dhu.edu.cn>
Date: Sun, 21 Mar 2021 00:20:21 +0800 (GMT+08:00)

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
leapin leap.solvate.in
# 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 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



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Received on Sat Mar 20 2021 - 09:30:02 PDT
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