[gmx-users] Problem with S-S bond

[Blaise Costa]

Hi Tsjerk, 
Thanks a lot. I tried writing a new message but it was bouncing back to me and I wrote to the administrator, and was suggested to register with GMX,which I already have done. 
 
Finally it worked when I replied for a previous message. However, sorry for the inconvenience, it will not happen again.
 
Thanks,
Blaise


----- Original Message ----
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, November 29, 2007 11:54:43 PM
Subject: Re: [gmx-users] Problem with S-S bond

Hi Blaise,

Disulfide bonds are only made when two Cys-S atoms are within 0.2 +/- 0.02 nm 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 2.16GHz Core 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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