AMBER Archive (2009)

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

From: Hopkins, Robert (hopkins_at_uhcl.edu)
Date: Sun Mar 29 2009 - 13:27:09 CDT

Wei, thanks for your comments on sleap. Without loading any
coordinate files, I tried sleap followed by
  source leaprc.ff99bsc0
to which I got the response:
  Error: can not find file leaprc.ff99bsc0 in all the search path
Then, I tried:
  source /usr/local/amber10/dat/leap/cmd/leaprc.ff99bsc0
to which I got the responses:
  Error: can not get bond for the given two atoms: CA H5
  Error: can not find atom C in molecule
  Error: can not find file frcmod.parmbsc0 in all the search path
  Error: can not find file DNA_CI in all the search path
When I then tried 'list', it appeared that all of the (deoxy- and
ribo-) nucleotides, amino acids, counterions and solvents were
present -- although I didn't check this carefully for the latter
categories.

After checking to be sure that the "search path" was *not* the
environment variable PATH for executables, I'm left with the
question: where can I find the "search path"? Also, although
I got the above Errors, It's not clear that they are actually
meaningful.

I'd really appreciate any further clarification that you might
be able to provide. Thanks!

Bob Hopkins

 

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
Behalf Of Wei Zhang
Sent: Saturday, March 28, 2009 6:29 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Problem reading PDB file into XLEAP - SLEAP

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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