AMBER Archive (2004)

Subject: AMBER: Xleap crash, problem with residue bonding

From: opitz_at_che.udel.edu
Date: Thu Jul 22 2004 - 09:24:35 CDT

('binary' encoding is not supported, stored as-is)

Dear Amber community,

I am working with a star polymer that I am building in xleap, in Amber 7.
I have defined the residues and they have worked in xleap before.
When connecting the residues I xleap the following:
tmp1 = sequence {cen arm1}
set tmp1 tail tmp1.1.y
tmp2 = sequence {tmp2 arm2}
etc.
When doing this the pdb as well as the results of an MD simulation viewed
in MOIL-View had the residues NOT connected and they had drifted apart in
the simultion.
Therefore I tried to connect the residues by telling leap specifically to
bond the atoms in question by using the bond command:
bond tmp1.1.y tmp1.2.x
bond tmp1.1.y tmp1.3.x
bond tmp1.1.z tmp1.4.x
etc.
I am able to save the library file using the saveoff command (this file I
will attach), but when I try to save the prmtop and inpcrd file using
saveamberparm xleap crashes.
It gives me the following error:
!FATAL ERROR----------------------------------------
!FATAL: In file [unitio.c], line 1763
!FATAL: Message: 1-4: cannot add bond 25 77
!
!ABORTING.

Can somebody please tell me what this error means and what I have to do
differently to be able to save prmtop and inpcrd files from the lib file
attached.
Thank you very much in advance.

Armin

P.S.: The attached file is a *.lib file. This seemed to cause the e-mail
to unsendable, therefore I just changed the file extension to *.out to be
able to send it.


  • application/octet-stream attachment: te8.out
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