[gmx-users] Re: [gmx-users]Missing disulfide bonds and LINCS Warning!
xiaobingtian at yahoo.com
Mon Mar 29 22:49:01 CEST 2004
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?
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
> 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 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
Phone: 215-955-1364 (Lab)
Do you Yahoo!?
Yahoo! Finance Tax Center - File online. File on time.
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