Hi,
Looks like you've stumbled onto input for my not-very-clever brute
force solvate wrapper script for LEaP:
https://github.com/drroe/Solvate.sh
You need to run that input with this script, not LEaP itself, e.g.
'Solvate.sh solvate.in'.
However, you may find that 'packmol' is a better alternative for you.
-Dan
On Sat, Mar 20, 2021 at 12:20 PM 库米尔 <418025.mail.dhu.edu.cn> wrote:
>
> 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
>
>
>
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 22 2021 - 07:30:03 PDT
