AMBER Archive (2007)

Subject: RE: AMBER: Disulfide Problem

From: Beale, John (jbeale_at_stlcop.edu)
Date: Thu Mar 01 2007 - 08:45:24 CST

Taking out the CONNECT and SSBOND lines in the pdb file seems to have
corrected the problem with LEaP crashing when I use the "bond" routine
on the SG atoms. I did change the CYS to CYX. Now, when I use the
"bond" routine the structure in the edit window shows up with the
correct disulfide bonds. The pdb file saved out of leap shows that the
disulfide bonds have become disconnected. This is also true of pdb files
generated with ambpdb using *.rst files from minimizations or dynamics
runs.

 

 

 

________________________________

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Carlos Simmerling
Sent: Thursday, March 01, 2007 8:15 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: Disulfide Problem

 

did you try taking out the CONNECT and SSBOND before loading into leap?
also check initial VDW energy in your first min- do the SG or HG show up
as
aotms with high gradients? that or high VDW energy are signs the SG are
too
close for vdw contact. Also did you change the CYS to CYX?

On 3/1/07, Beale, John <jbeale_at_stlcop.edu> wrote:

I have a little more information about my disulfide bond problem. Dr.
Case mentioned that the problem with LEaP crashing after the "bond"
command to form disulfides might mean that these bonds are already
present. I did a little investigating. When I load my pdb file into LEaP
and view it in the edit window, all of the disulfide bonds are properly
connected. If I just avoid using the "bond" command, saveAmberParm
writes the *.top and *.crd files normally. If, while still in LEaP, I
save the pdb file (savePdb), when I look at the pdb in Chimera the
disulfide bonds are broken. So, somewhere in the process of writing that
pdb file from LEaP the information that is needed to connect the
disulfide bonds is lost. The pdb file that is saved from LEaP is
stripped of SSBOND and CONNECT lines, so maybe it's no surprise that
these S - S connectivities are lost.

 

My question is this- should I just assume, since the disulfide bonds are
present in the edit screen in LEaP, that these bonds are really there
and that I don't need to worry about using the "bond" procedure for SG -
SG?

 

Another problem is that when I convert the *.rst files output by
minimization or MD to pdb files, once again the disulfides show up as
not connected. The two sulfur atoms, however, seem to stay in close
relationship to each other.

 

Thanks,

 

John

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