AMBER Archive (2007)

Subject: Re: AMBER: Disulfide Problem

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Mar 02 2007 - 08:54:42 CST

yes, this is correct, I assumed that the user would use the bond command
since
they had already stated that. My suggestions were to be done in addition to
the bond command.
thanks for the clarification!

On 3/2/07, xiaoqin huang <xqhuang1018_at_msn.com> wrote:
>
> 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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