[gmx-users] Re: [gmx-users]Missing disulfide bonds and LINCS Warning!

[David]

On Mon, 2004-03-29 at 22:47, xiaobing tian wrote:
> Dear David,
>  
> I just specified the flag -cys. But pdb2gmx showed "unknown argument
> -cys"
> Then i tried flag -ss, it resulted wrong bonds that containd carbon
> atoms and were 
> protonated. What were wrong with that?

pdb2gmx uses a definition of an SS bond that has a distance of 0.2 nm
with a tolerance of 10 %. The SS bonds that are not formed automatically
fall outside this range as you can see in the matrix that is printed. If
you put a copy of the library file specbond.dat in your working
directory and edit the tolerance for the SS bond that should work.
>  
> Thanks again,
>  
> Xiaobing Tian
> 
> David <spoel at xray.bmc.uu.se> wrote:
>         On Mon, 2004-03-29 at 21:43, xiaobing tian wrote:
>         > 
>         > Dear Gromacs users,
>         > 
>         > 
>         > 
>         > I made a position-restrained MD simulation with protein
>         1AZ8. The
>         > simulation terminated prematurely due to a bunch of Lincs
>         Warnings (
>         > started about from the steps 5000). 
>         > 
>         
>         you have to check when running pdb2gmx whether all disulfide
>         bonds are
>         made. if not you need to specify a flag -cys to make the bonds
>         interactively.
>         > 
>         > 
>         > When I prepared the protein PDB file, I deleted the drug
>         that bound to
>         > it and water molecules. I have kept the CONNETCTIONs for
>         disulfide
>         > bonds on the PDB file. The six disulfide bonds of the
>         protein were
>         > correctly displayed on Rasmol, PDB viewer and AutoDock Tool.
>         But when
>         > I used VMD to check the file, the four disulfide bridges
>         among the six
>         & gt; were missing in the PDB file. I was able to produce .top
>         and .gro
>         > files with pdb2gmx (v. 3.2.1), using Gromacs force field,
>         and go on
>         > the MD simulation till the Lincs Warnigs occurred.
>         > 
>         > 
>         > 
>         > I have checked the .gro file produced from pdb2gmx and other
>         .gro
>         > files by VMD, all of them showed several abnormal and wrong
>         bonds or
>         > atom groups formed between those disulfide atoms. Is this
>         the cause
>         > that resulted in Lincs Warnings and premature termination of
>         MD? How
>         > to fix this problems?
>         > 
>         > 
>         > 
>         > Thank you very much in advance.
>         > 
>         > 
>         > 
>         > Xiaobing Tian
>         > 
>         > 
>         > 
>         > Xiaobing Tian Ph.D.
>         > Department of Microbiology and Immunology
>         > Thomas Jefferson University
>         > 1025 Walnut St., Suite 420
>         > Philadelphia, PA19107
>         > Phone: 215-955-1364 (Lab)
>         > 
>         > 
>         >
>         ______________________________________________________________________
>         > Do you Yahoo!?
>         > Yahoo! Finance Tax Center - File online. File on time.
>         -- 
>         David.
>         ________________________________________________________________________
>         David van der Spoel, PhD, Assist. Prof., Molecular Biophysics
>         group,
>         Dept. of Cell and Molecular Biology, Uppsala University.
>         Husargatan 3, Box 596, 75124 Uppsala, Sweden
>         phone: 46 18 471 4205 fax: 46 18 511 755
>         spoel at xray.bmc.uu.se spoel at gromacs.org
>         http://xray.bmc.uu.se/~spoel
>         ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>         
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> 
> 
> Xiaobing Tian Ph.D.
> Department of Microbiology and Immunology
> Thomas Jefferson University
> 1025 Walnut St., Suite 420
> Philadelphia, PA19107
> Phone: 215-955-1364 (Lab)
> 
> 
> ______________________________________________________________________
> Do you Yahoo!?
> Yahoo! Finance Tax Center - File online. File on time.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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