Dr. Case -- Here's a quick response to your comment regarding sleap. I'm running Cygwin (1.5.25-15)
with Windows Vista Home Premium on a Fujitsu Lifebook A Series notebook. When I type the command
to initiate tleap, I get the following output when loading leaprc.ff99bsc0:
-I: Adding /usr/local/amber10/dat/leap/prep to search path.
-I: Adding /usr/local/amber10/dat/leap/lib to search path.
-I: Adding /usr/local/amber10/dat/leap/parm to search path.
-I: Adding /usr/local/amber10/dat/leap/cmd to search path.
Welcome to LEaP!
Sourcing leaprc: /usr/local/amber10/dat/leap/cmd/leaprc
Log file: ./leap.log
Loading parameters: /usr/local/amber10/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /usr/local/amber10/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading parameters: /usr/local/amber10/dat/leap/parm/frcmod.parmbsc0
Reading force field modification type file (frcmod)
Reading title:
modifies parm99 for nucleic acids: see http://mmb.pcb.ub.es/PARMBSC0/
Loading library: /usr/local/amber10/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber10/dat/leap/lib/DNA_CI.lib
Loading library: /usr/local/amber10/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber10/dat/leap/lib/solvents.lib
>
Alternatively, when I type sleap, I get only the following:
[gtkleap]$
I hadn't realized that this may indicate a potential bug. Thanks again for your help.
Bob Hopkins
_____
From: amber-bounces.ambermd.org on behalf of David A. Case
Sent: Sat 3/28/2009 8:28 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Problem reading PDB file into XLEAP
On Fri, Mar 27, 2009, Hopkins, Robert wrote:
> I'll have to put in more time in trying
> to use sleap since I haven't yet figured out how to easily source in all
> the parameter files needed.
sleap is supposed to be a drop-in replacement for tleap. If it doens't
work that way, it is probably a bug, and should be reported.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Mar 29 2009 - 01:18:00 PDT
