AMBER Archive (2002)

Subject: RE: bondbydistance

From: Nicholson, James D Mr ARO (James.Nicholson_at_apg.amedd.army.mil)
Date: Sat Sep 07 2002 - 19:16:28 CDT

Try running the pdb file through babel, converting from PDB to PDB. Leap
isn't as versatile as other programs in what it will accept.

-Jim N.

-----Original Message-----
From: case [mailto:case_at_scripps.edu]
Sent: Friday, September 06, 2002 8:04 PM
To: amber; eric hu
Subject: RE: bondbydistance

>===== Original Message From eric hu <erichu_linux_at_yahoo.com> =====
>I load a pdb file to tleap and try to make a lib file.
>But the bondbydistance does not generate any bonds.
>The structure looks fine when I use rasmol or swisspdb
>to view the pdb file.
>

Try different pdb files to see if this is a universal problem for you. See
if a small pdb file also fails. I have not seen your problem, so the code
works, at least with my pdb files and my machine/OS.

If you still can't see what is wrong with your pdb file, please post it, or
a small part of it.

...regards...dac

==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================