[gmx-users] Problem with S-S bond

[Tsjerk Wassenaar]

Hi Blaise,

Disulfide bonds are only made when two Cys-S atoms are within 0.2 +/-
0.02nm from each other. This distance is in the file
specbond.dat. You can search the archives for how to make the bond.

Also, please start a new thread rather than replying to a message. Now
there's debris unrelated to your question, which is a bit annoying.

Cheers,

Tsjerk

On Nov 30, 2007 12:41 AM, Blaise Costa <blaisecosta at yahoo.com> wrote:

>  Hello Gromacs users,
> I have docked an antagonist into the agonist bound conformation and doing
> MDS to get the antagonist bound conformation after several nS simulation.
> Therefore expected that the protein might undergo big conformational
> changes, and running the simulation in "Unconstrained Start = Yes" . While
> starting the simulation the S atoms were close enough (3A<) to make the
> disulphide bond. Now, after 1.5 nS, noticed that it is deviated for more
> than 6.5A, therefore no way to make the bond. Is there any way that I can
> give constraint for these bonds and can I restart the program from last
> point?
>
> I gave -SS command during pdb2gmx, believed that gromacs will keep the S
> atoms close enough to make the S-S bond. I am using Gromacs version 3.3.1!
>
> Many thanks in advance!
>
> Blaise
>
>
> ----- Original Message ----
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Thursday, November 29, 2007 12:29:57 PM
> Subject: Re: [gmx-users] Double precision test failure
>
> Chris Snook wrote:
> > I am trying to use gromacs on a Mac OS X 10.4.11 with an Intel 2.16GHzCore 2
> > Duo processor.
> >
> > I have downloaded and installed the v 3.3.2 binaries of gromacs for this
> OS and
> > run the test program. The single precision tests run OK. But the double
> > precision tests completely fail with the following output (partial):
> >
> > No topol.tpr file in angles1. grompp failed
> > FAILED. Check files in angles1
> > No topol.tpr file in angles125. grompp failed
> > FAILED. Check files in angles125
> > No topol.tpr file in bham. grompp failed
> > FAILED. Check files in bham
> > etc
> > No topol.tpr file in kernel334. grompp failed
> > FAILED. Check files in kernel334
> > 63 out of 63 kernel tests FAILED
> > readline() on closed filehandle PIPE at ./gmxtest.pl line 353.
> > etc
> >
> > I've checked the archives and the manual and haven't seen anything
> relevant to
> > this. Any help would be appreciated.
>
> did you source GMXRC?
> >
> > Regards
> >
> > Chris
> >
> > _______________________________________________
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>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se    spoel at gromacs.org  http://folding.bmc.uu.se
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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