Hello Matias
Thanks a lot for the typo catch! Seems like staring at the screen for long hours is causing me to make such terrible errors!
Thanks again.
Debarati
From: Matias Machado<mailto:mmachado.pasteur.edu.uy>
Sent: 11 November 2021 18:18
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] tleap problem
Dear Debarati,
The command "saveamberparam" is misspelled, it is "saveamberparm", and command "go" doesn't exist in leap (use "help" command to see the available options)
Best,
Matías
----- Mensaje original -----
De: "Debarati DasGupta" <debarati_dasgupta.hotmail.com>
Para: "AMBER.ambermd.org" <amber.ambermd.org>
Enviados: Jueves, 11 de Noviembre 2021 18:11:51
Asunto: [AMBER] tleap problem
source leaprc.gaff2
source leaprc.water.tip3p
loadamberparams SRO.frcmod
loadamberprep SRO.prepi
com=loadpdb SRO.pdb
charge com
addions com Cl- 0
saveamberparam com ligand.prmtop ligand.inpcrd
go
This is my input file for preparing a ligand prmtop file for mmpbsa.
This is the strange error I see:
[debarati.login02 mmpbsa]$ tleap -f test.in
-I: Adding /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/dat/leap/prep to search path.
-I: Adding /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/dat/leap/lib to search path.
-I: Adding /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/dat/leap/parm to search path.
-I: Adding /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/dat/leap/cmd to search path.
-f: Source test.in.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./test.in
----- Source: /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/dat/leap/cmd/leaprc.gaff2
----- Source of /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/dat/leap/cmd/leaprc.gaff2 done
Log file: ./leap.log
Loading parameters: /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
----- Source: /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/dat/leap/cmd/leaprc.water.tip3p
----- Source of /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/dat/leap/cmd/leaprc.water.tip3p done
Loading library: /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/dat/leap/lib/atomic_ions.lib
Loading library: /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/dat/leap/lib/solvents.lib
Loading parameters: /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/dat/leap/parm/frcmod.tip3p
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP3P water
Loading parameters: /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/dat/leap/parm/frcmod.ions1lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set)
Loading parameters: /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008)
Loading parameters: /cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/dat/leap/parm/frcmod.ions234lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set)
Loading parameters: ./SRO.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Loading Prep file: ./SRO.prepi
Loading PDB file: ./SRO.pdb
total atoms in file: 26
Total unperturbed charge: 1.000000
Total perturbed charge: 1.000000
1 Cl- ion required to neutralize.
Adding 1 counter ions to "com" using 1A grid
Grid extends from solute vdw + 2.51 to 8.42
Resolution: 1.00 Angstrom.
(no solvent present)
Calculating grid charges
Placed Cl- in com at (-11.33, -7.00, -9.49).
Done adding ions.
/cm/shared/apps/spack/cpu/opt/spack/linux-centos8-zen2/gcc-10.2.0/amber-external/bin/teLeap: Fatal Error!
Error from the parser: syntax error, unexpected LVARIABLE, expecting LASSIGN
Exiting LEaP: Errors = 1; Warnings = 0; Notes = 0.
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Received on Thu Nov 11 2021 - 17:30:02 PST
