AMBER Archive (2009)

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

From: Wei Zhang (zgjzweig_at_gmail.com)
Date: Sat Mar 28 2009 - 18:29:20 CDT

Hi Robert,

     sleap does not print that much information as tleap/xleap while
loading parameters, but it does load everything. You can try
to type in:

     list

after

    source leaprc.ff99BSC0

and you will see all the residues etc.

     Sincerely,

     Wei

On Mar 28, 2009, at 6:12 PM, Hopkins, Robert wrote:

> 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_at_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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