[gmx-users] Re: [gmx-users]Missing disulfide bonds and LINCS Warning!
spoel at xray.bmc.uu.se
Mon Mar 29 22:59:01 CEST 2004
On Mon, 2004-03-29 at 22:47, xiaobing tian wrote:
> Dear David,
> I just specified the flag -cys. But pdb2gmx showed "unknown argument
> 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
> > When I prepared the protein PDB file, I deleted the drug
> that bound to
> > it and water molecules. I have kept the CONNETCTIONs for
> > 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
> > 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
> 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
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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 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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