[gmx-users] Ryckeart Bellemans parameters for Fe coupled to cystines

Anton Feenstra feenstra at chem.vu.nl
Tue Dec 23 08:15:05 CET 2003


saurabh shakya wrote:

> Hi ,
> I forgot to mention in my last posting that the md
> simulation is running fine for the system in vaccum
> but only when i hydrate it i run across the lincs
> warning .

Have you checked it by any chance water(s) are located anywhere near
your iron and/or cysteine? Genbox may put water in large enough cavities
inside your protein, or they may diffuse there during the simulation.
Can you energy minimize your solvated conformation?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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