RE: AMBER: Disulfide Problem

From: Kristina Furse <>
Date: Thu, 1 Mar 2007 11:19:17 -0500

Just a thought. When you say "The pdb file saved out of leap shows that the
disulfide bonds have become disconnected." what are you using to view that pdb?
I believe different viewers use different criteria when assigning bonds by
distance when there are no official connect records in the pdb file. The
disulfide bond is a slightly longer bond, so maybe the viewer just isn't
picking it up? Also, if you are reading the pdb you wrote with leap back into
leap to view it in the edit window, you will need to make the bond again since
I don't think the pdbs leap writes have explicit connect records.

Good luck!

Quoting "Beale, John" <>:

> 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: [] On Behalf
> Of Carlos Simmerling
> Sent: Thursday, March 01, 2007 8:15 AM
> To:
> 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 <> 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
> ==================

Kristina Furse
Postdoctoral Research Associate
262 Stepan Chemistry Hall
Notre Dame, IN 46556
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Received on Sun Mar 04 2007 - 06:07:39 PST
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