Re: [AMBER] error

From: Matias Machado <>
Date: Fri, 07 Aug 2020 10:00:06 -0300 (UYT)

Dear Ayesha Fatima,

Is there any chance you are generating the file "" in Windows and then running in Linux?

My guess is that you may be facing Linux/Windows compatibility issues due to the "carriage return", which may be interpreted as an extra argument by leap. Hence the error "Improper number of arguments!" despite "not seeing" the character in the line...

In Linux you can unmask the issue by executing:

cat -A

then you should see...

source leaprc.protein.ff14SB ^M$

If that's the case, then check this link for possible solutions...

Best regards,


PS: the fact of sending the mail from a Windows 10 computer gave me the hint Watson... ;-)

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

----- Mensaje original -----
De: "Ayesha Fatima" <>
Para: "AMBER Mailing List" <>
Enviados: Jueves, 6 de Agosto 2020 13:41:19
Asunto: [AMBER] error

 Good morning everyone,

I created a file and wanted to run it but it keeps giving me the
syntax error or

-I: Adding /mnt/d/amber/amber18/dat/leap/prep to search path.
-I: Adding /mnt/d/amber/amber18/dat/leap/lib to search path.
-I: Adding /mnt/d/amber/amber18/dat/leap/parm to search path.
-I: Adding /mnt/d/amber/amber18/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source

Welcome to LEaP!
Sourcing: ./

/mnt/d/amber/amber18/bin/teLeap: Fatal Error!
source: Improper number of arguments!
usage: source <filename>

my file has the following entries


source leaprc.protein.ff14SB
source leaprc.gaff2
source leaprc.water.tip3p
loadamberparams frcmod.ionsjc_tip3p
set default PBradii mbondi3
rec=loadpdb rec.pdb
loadamberparams bras.frcmod
lig=loadmol2 bras.mol2
gascomplex= combine {rec lig}
savepdb gascomplex bras.complex.pdb
saveamberparm gascomplex bras.gas.complex.prmtop bras.gas.complex.rst7
saveamberparm rec bras.gas.receptor.prmtop bras.gas.receptor.rst7


i used the command

tleap -f

Am i doing anything wrong?

Thank you for your guidance



Sent from Mail <> for Windows
AMBER mailing list

AMBER mailing list
Received on Fri Aug 07 2020 - 06:30:02 PDT
Custom Search