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

xiaobing tian xiaobingtian at yahoo.com
Mon Mar 29 21:46:01 CEST 2004

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). 


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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20040329/45884a89/attachment.html>

More information about the gromacs.org_gmx-users mailing list