AMBER Archive (2007)

Subject: Re: AMBER: Disulfide Problem

From: xiaoqin huang (xqhuang1018_at_msn.com)
Date: Fri Mar 02 2007 - 08:48:14 CST

Even loading a pdb with CYS changed into CYX, the Leap cannnot keep S-S bond
connected when you save the top and crd file using the command
"saveamberparm". what you do is using the command "bond" before you save
your top and crd file. Only in this way, the S-S bond will be there no
matter you do minimization or MD.
I always do this way afte testing.

>From: "Carlos Simmerling" <carlos.simmerling_at_gmail.com>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: Disulfide Problem
>Date: Thu, 1 Mar 2007 09:15:22 -0500
>
>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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