AMBER Archive (2007)

Subject: AMBER: LEaP crashes

From: Beale, John (jbeale_at_stlcop.edu)
Date: Wed Feb 28 2007 - 10:29:16 CST

I am trying to set up a protein that contains 7 disulfide bonds. I have
changed the name CYS to CYX in the pdb file. When I view the pdb file (I
use Chimera to visualize) all of the disulfide bonds are connected. When
I load the pdb file into LeAP it loads normally, and when I look at the
file in the unit editor all of the disulfide bonds are present. At this
point if I use the "check" command LeAP tells me that the "unit is OK".

 

Now, if I do a "savePdb" and look at the output the disulfide bonds are
broken. At this point if I "saveAmberParm" the *.top and *.crd files are
saved normally.

 

The problem arises when I try to bond the disulfide bonds in LeAP. I use
the correct commands (bond npo.10.sg npo.54.SG, for example). After I
have set up all the disulfide bonds, when I try to execute a
"saveAmberParm" LeAP crashes with the following message:

 

! FATAL ERROR

! FATAL: In file [unitio.c], line 1769

! FATAL: Message: 1-4: cannot add bond 104 701

!

! ABORTING

 

I have played around with this and I have found that this error happens
even if I try to bond as few as one of the disulfides.

 

I am using AMBER 9, ff03. I have applied all of the bugfixes to the
installation.

 

Does anyone know what this error means and how I can work through it?

 

JB

 

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