AMBER Archive (2007)

Subject: Re: AMBER: Problem with xLeap

From: alfredoq_at_mail.fcq.unc.edu.ar
Date: Tue Nov 13 2007 - 11:07:40 CST

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.
Thank you very much
Alfredo Quevedo

Quoting "David A. Case" <case_at_scripps.edu>:

> On Tue, Nov 13, 2007, alfredoq_at_mail.fcq.unc.edu.ar wrote:
>
>> I am writting in order to ask for some hint about a
>> problem with xLeap. The point is that when I load a force field, for example
>> ff99, and after trying to edit any residue, I see the molecule in a 2D plain
>> view.
>
> I'm not sure I can tell what you mean by "2D plain view". Can you give the
> exact commands you used for xleap, and a better description of what
> appears on
> the screen? Can you rotate the molecule around using the mouse? Do the bond
> lengths and angles look correct?
>
> ...dac
>
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Facultad de Ciencias QuĂmicas - Universidad Nacional de CĂrdoba


ALA.jpg

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