Dear Dr. Case: Regarding the warnings related to "fonts" I solved them
intalling
additional fonts.
When I start xleap, I get the following:
Welcome to LEaP!
(no leaprc in search path)
Sourcing: /home/general/Programas/amber9/dat/leap/cmd/leaprc.ff99
Log file: ./leap.log
Loading parameters: /home/general/Programas/amber9/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading library: /home/general/Programas/amber9/dat/leap/lib/all_nucleic94.lib
Loading library: /home/general/Programas/amber9/dat/leap/lib/all_amino94.lib
Loading library: /home/general/Programas/amber9/dat/leap/lib/all_aminoct94.lib
Loading library: /home/general/Programas/amber9/dat/leap/lib/all_aminont94.lib
Loading library: /home/general/Programas/amber9/dat/leap/lib/ions94.lib
Loading library: /home/general/Programas/amber9/dat/leap/lib/solvents.lib
It is the first time I get the "(no leaprc in search path)" message,
may be this
causing the problems
Thank you again for the help
Alfredo Quevedo
Quoting "David A. Case" <case.scripps.edu>:
> On Tue, Nov 13, 2007, alfredoq.mail.fcq.unc.edu.ar wrote:
>
>> Dear Dr. Case: I start xleap with the command "xleap -s -f leaprc.ff99"
>> the following appears in the console window:
>>
>> [general.localhost ~]$ xleap -s -f leaprc.ff99
>> -I: Adding /home/general/Programas/amber9/dat/leap/prep to search path.
>> -I: Adding /home/general/Programas/amber9/dat/leap/lib to search path.
>> -I: Adding /home/general/Programas/amber9/dat/leap/parm to search path.
>> -I: Adding /home/general/Programas/amber9/dat/leap/cmd to search path.
>> -s: Ignoring startup file: leaprc
>> -f: Source leaprc.ff99.
>> Warning: Cannot convert string "-*-helvetica-medium-r-*-*-18-*-*-*-*-*-*-*"
>> to
>> type FontStruct
>> Warning: Cannot convert string "-*-helvetica-bold-r-*-14-*" to type
>> FontStruct
>> Warning: Cannot convert string "-*-helvetica-medium-o-*-*-14-*-*-*-*-*-*-*"
>> to
>> type FontStruct
>> Warning: Cannot convert string "-*-courier-bold-r-*-*-14-*-*-*-*-*-*-*"
>> to type
>> FontStruct
>> Warning: Cannot convert string "-*-helvetica-medium-o-*-*-18-*-*-*-*-*-*-*"
>> to
>> type FontStruct
>> Warning: Cannot convert string "-*-courier-medium-r-*-*-14-*-*-*-*-*-*-*" to
>> type FontStruct
>>
>>
>> I can rotate the molecule, but only in two planes. I see a two dimensional
>> (flat) view of the molecule, for example the ALA residue. I am attaching the
>> image.
>
> Did you type anything at the command prompt (such as "edit ALA")? Did you
> do anything in the window but rotate the molecule?
>
> Something is clearly quite wrong, but I don't know what. The colors of the
> atoms are all wrong (as if the atom types were un-recognized). Does
> your LEaP
> pass the test cases? What operating system and compiler are you using?
>
> ....dac
>
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Received on Wed Nov 14 2007 - 06:07:49 PST
