[gmx-users] Re: Segmentation fault 4

[Anton Feenstra]

Tanos C. C. França wrote:
> Hi  Anton !!!!!!!!! 
> It´s the protein docked with its cofactor and coenzyme. There are two
> active sites with one cofactor and one coenzyme in each one. I have
> already checked the structure in ProChek and everything is OK. I have
> also performed one round of steep descent EM until emtol = 1000 and
> further 1000 steps of cg.  I suspect that the problem is really the
> molecules docked to the actives sites cause without then the dynamics
> went well. I am looking now for any mistakes committed in the
> parametrization and docking process.

Try a simple minimization of your cofactor and coenzyme in vacuum. If
that works, try some MD of these molecules, also in vacuum. While this
is not physically realistic, you can from the behaviour see if there
might be errors in your topology.

>             There is another detail in my job. I had to add 12 atoms of
> Na+ to neutralize the system. Could this create any problem ?  If so, is
> it acceptable to run the job without neutralize the system ???????

That depends. I do it sometimes, but then I also still use cut-offs.
But a wrong placement of your Na+ ions can defenitely cause problems.
How did you add them? Did you look at them in detail?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|