Re: [AMBER] TLEAP error

From: Subashini .K <>
Date: Thu, 12 Jan 2017 14:39:55 +0000


When the following commands were executed,

source leaprc.ff14SB
loadAmberParams frcmod.tip4pew
loadAmberParams frcmod.ionsjc_tip4pew
source leaprc.gaff
LIG = loadmol2 LIG.mol2
loadamberparams LIG.frcmod
check LIG
receptor = loadPDB rec_final.pdb
complex = combine {receptor LIG}
set default PBRadii mbondi2
saveAmberParm LIG LIG.crd
receptor = loadPDB rec_final.pdb
saveAmberParm receptor rec.crd
saveAmberParm complex com.crd
savepdb complex complex_gas.pdb
charge complex
addIons2 complex Na+ 0
solvateBox complex TIP4PBOX 10.0
saveAmberParm complex com_solvated.crd
savepdb complex com_solvated.pdb

The output file was obtained.

But, when this command was given

tleap -s -f tleap.all ERROR: syntax error

it shows an error

I am using AMBERTOOLS 15



From: David Case <>
Sent: Thursday, January 12, 2017 6:47 PM
To: AMBER Mailing List
Subject: Re: [AMBER] TLEAP error

On Thu, Jan 12, 2017, Subashini .K wrote:

> tleap -s -f tleap.all ERROR: syntax error

We would need to see the complete "tleap.all": there is a mistake somewhere in

> source leaprc.ff14SB

As pointed out elsehwere, this needs to be upated for AmberTools16, but this
line should not be giving a syntax error. So I suspect that there is a
problem somewhere else in the input file. Please examine the output and log
files carefully: they are usually pretty good at identifying where the error
is; usually less good in explaining how to fix it.


AMBER mailing list
AMBER -- AMBER Mailing List<>
AMBER -- AMBER Mailing List About AMBER: This is the AMBER Mailing List. It is designed to provide a forum for users of the AMBER Molecular Dynamics and related ...

AMBER mailing list
Received on Thu Jan 12 2017 - 07:00:03 PST
Custom Search