[gmx-users] inactive - active conversion

[Anton Feenstra]

Daan Virtual wrote:
> Dear John
> 
> I think what you are asking is how you can create a starting model for the
> all trans retinal? There are a few ways of doing this.

Also, there are versions of Rasmol that allow you to rotate (i.e.
modify) a selected dihedral angle and write a .pdb file with the
new coordinates.

You might also need a modified topology, if the dihedral you rotate
is defined as an improper (to keep it planar). You will need to
change the order of the atoms on which it is defined to shift the
minimum to your desired conformation.


-- 
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)                               |
|_____________|_______________________________________________________|