If you are still using amber9, I suggest upgrading.
Now to look at one of your problems:
> loadamberparams /usr/local/amber9/dat/leap/parm/gaff.dat
> loadAmberParams: Improper number of arguments!
How to figure it out? Ask leap for help:
Welcome to LEaP!
(no leaprc in search path)
> help loadamberparams
variable = loadAmberParams filename
PARMSET _variable_
STRING _filename_
Load an AMBER format parameter set file and place it in _variable_.
All interactions defined in the parameter set will be contained within
_variable_. This command causes the loaded parameter set to be included
in LEaP's list of parameter sets that are searched when parameters are
required. General proper and improper torsion parameters are modified,
the AMBER general type "X" is replaced with the LEaP general type "?".
Bill
On 7/17/17 8:55 AM, Dey, S. wrote:
> Hi,
>
> I am trying to generate topology for FAD ligand (Flavin Adenine
> Dinucleotide) using Ambertools 16.
>
> So, I generated resp charges after running Gaussian and also generated
> frcmod using parmchk. However, as I am trying to run LEaP, it is showing
> error. I am using the following code in my leap.in file:
>
> * source /usr/local/amber9/dat/leap/cmd/leaprc.gaff *
>
> * loadamberparams /usr/local/amber9/dat/leap/parm/gaff.dat*
>
> * M = loadmol2 name.mol2*
>
> * mods = loadamberparams frcmod *
>
> * saveamberparm M prmtop inpcrd*
>
> * quit*
>
>
> However, it is showing error message :
>
>
> *teLeap -f leap.in <http://leap.in/>*
> *-f: Source leap.in <http://leap.in/>.*
>
> *Welcome to LEaP!*
> *(no leaprc in search path)*
> *Sourcing: ./leap.in <http://leap.in/>*
> *ERROR: syntax error*
>
> *: not foundpen file leaprc.gaff*
> *loadAmberParams: Improper number of arguments!*
> *usage: <variable> = loadAmberParams <filename>*
> *: not foundpen file fad.mol2*
> *saveAmberParm: Argument #1 is type String must be of type: [unit]*
> *usage: saveAmberParm <unit> <topologyfile> <coordfile>*
> *ERROR: syntax error*
>
> So, can someone tell me what is the problem with this and how to solve this
> out?
>
> With regards,
> Souvik
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Received on Mon Jul 17 2017 - 10:00:02 PDT
