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 - 06:07:50 PST
