On May 23, 2014, at 2:05 AM, amin.imtech.res.in wrote:
>
>
> Dear all,
>
> I am trying to use the zinc parameters from Yuan-Ping Pang. I have
> copied the files into the respective directories. When i try to source
> leaprc.zinc, I get errors like this :
>
> Log file: ./leap.log
>>> #
>>> # loading force field parameters for the tetrahedraon-shaped zinc divalent cation
>>> #
>>> addAtomTypes { { "DZ" "Zn" "sp3" } { "Zn" "Zn" "sp3" } }
> addAtomTypes: Improper number of arguments!
> usage: addAtomTypes <list_of_lists>
>>> loadOff znb.lib
> Could not open file znb.lib : not found
> Could not open database: znb.lib
>>> loadOff hin.lib
> Could not open file hin.lib : not found
> Could not open database: hin.lib
>>> loadOff hydroxide.lib
> Could not open file hydroxide.lib : not found
> Could not open database: hydroxide.lib
>>> loadamberparams frcmod.zinc
> Could not open file frcmod.zinc : not found
>>
>> exit
>
> I have placed the lib files in $AMBERHOME/dat/leap/lib and frcmod file
> in $AMBERHOME/dat/leap/parm.
>
> I can load the other leaprc files present in this directory without any
> problem. Can someone please help me with this?
Why not put the files in the same directory you are running tleap in? That said, these errors do not make sense. The addAtomTypes syntax looks correct, and anything in $AMBERHOME/dat/leap/* should be in the default search paths for tleap and xleap.
The only possible problem I can imagine is that your file has DOS line endings (carriage returns, or \r\n) instead of newlines (just \n). If this is the case, it may be parsing the last character of every command with a trailing \r which would not appear on the screen or error message, but would prevent files from being found or lists from being terminated. This is all speculation, though.
Try running every file you downloaded through the dos2unix program (which modifies files in-place, getting rid of carriage return endings). For example:
dos2unix znb.lib
dos2unix hin.lib
dos2unix hydroxide.lib
dos2unix frcmod.zinc
dos2unix leaprc.whatever
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 23 2014 - 05:30:03 PDT
