[gmx-users] using .pdb file from protein data bank

[Anton Feenstra]

David wrote:

> On Thu, 2004-01-15 at 19:03, Madhuri Agashe wrote:
> 
>>Hi,
>>I want to use a pdb file from the protein data bank and run a MD simulation
>>on it.
>>
>>How does gromacs treat the pdb file taken directly from the protein data
>>bank? Are protonation sites checked or protonation/deprotonation done?

pdb2gmx will check histidines for hydrogen bonding partners and adjust
protonation accordingly. IIRC, that is the extent of checking protonation.

A protocol I use routinely on x-ray (pdb) structures is:
1) EM protein in vacuum
2) add water (genbox)
3) EM protein + water
4) MD water (position restraints on protein) for 1ps
5) production MD.

This works for me for any pdb file I tried it on till now (several tens).


-- 
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)                               |
|_____________|_______________________________________________________|