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

[xiaobing tian]

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?
 
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
> 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)

---------------------------------
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