On Tue, Jul 15, 2014 at 2:13 AM, Suchetana Gupta <suchetana.gupta.gmail.com>
wrote:
> Dear Amber users
> I am using Amber12. I am noticing one error very recently, which was not
> happening earlier. I am trying to perform minimisation and equilibration of
> a protein-inhibitor complex. When I am using the command tleap -s -f
> leap.in to
> run LEaP, I am getting the following error:
>
> -I: Adding /usr/local/bin/amber12//dat/leap/prep to search path.
> -I: Adding /usr/local/bin/amber12//dat/leap/lib to search path.
> -I: Adding /usr/local/bin/amber12//dat/leap/parm to search path.
> -I: Adding /usr/local/bin/amber12//dat/leap/cmd to search path.
> -s: Ignoring startup file: leaprc
> -f: Source leap.in.
>
> Welcome to LEaP!
> Sourcing: ./leap.in
> : not foundpen file leaprc.ff99SB
> : not foundpen file leaprc.gaff
> : not foundpen file tmc.frc
> : not foundpen file tmc.prep
> : not foundpen file min3.pdb
> solvateBox: Argument #1 is type String must be of type: [unit]
> usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
> check: Argument #1 is type String must be of type: [unit molecule residue
> atom]
> usage: check <unit> [parmset]
> charge: Argument #1 is type String must be of type: [unit molecule residue
> atom list]
> usage: charge <object>
> addIons: Argument #1 is type String must be of type: [unit]
>
> addIons unit ion1 #ion1 [ion2 #ion2]
>
> UNIT _unit_
> UNIT _ion1_
> NUMBER _#ion1_
> UNIT _ion2_
> NUMBER _#ion2_
>
> Adds counterions in a shell around _unit_ using a Coulombic potential
> on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
> opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
> the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
> If solvent is present, it is ignored in the charge and steric calculations,
> and if an ion has a steric conflict with a solvent molecule, the ion is
> moved to the center of said molecule, and the latter is deleted. (To
> avoid this behavior, either solvate _after_ addions, or use addIons2.)
> Ions must be monoatomic. Note that the one-at-a-time procedure is not
> guaranteed to globally minimize the electrostatic energy. When neutralizing
> regular-backbone nucleic acids, the first cations will generally be added
> between phosphates, leaving the final two ions to be placed somewhere
> around
> the middle of the molecule.
> The default grid resolution is 1 Angstrom, extending from an inner radius
> of (max ion size + max solute atom size) to an outer radius 4 Angstroms
> beyond. A distance-dependent dielectric is used for speed.
>
>
> savePdb: Argument #1 is type String must be of type: [unit]
> usage: savePdb <object> <filename>
> saveAmberParm: Argument #1 is type String must be of type: [unit]
> usage: saveAmberParm <unit> <topologyfile> <coordfile>
> ERROR: syntax error
>
> ERROR: syntax error
>
> >
> However, when I am doing it separately, line by line, as in, tleap
> source leaprc.ff99SB and so on, it is working fine and proper topology and
> crd files are generated.
> I wonder what is happening that is preventing tleap -s -f from working for
> me.
>
I've never had problems running a leap script via "tleap -f leap.in" as
opposed to typing the commands in one-by-one. It _seems_ to me that tleap
is interpreting your script correctly, but it just can't find any of the
files. Maybe your file has DOS line endings (are you running on Windows)?
Is tleap somehow getting run from a different directory than where your
files are?
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jul 15 2014 - 09:00:04 PDT
