AMBER Archive (2007)

Subject: Re: AMBER: Problem with xLeap

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 13 2007 - 11:55:24 CST

On Tue, Nov 13, 2007, alfredoq_at_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_at_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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu