RE: [AMBER] Problem reading PDB file into XLEAP - SLEAP

From: Hopkins, Robert <hopkins.uhcl.edu>
Date: Sat, 28 Mar 2009 23:12:06 +0000

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


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Received on Sun Mar 29 2009 - 01:18:00 PDT
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