[gmx-users] coordinate file is mandatory?

[Anton Feenstra]

Rongliang Wu wrote:

> Hello gmx-users,
>        since after EM the output coordinate file follows what the top file signifies, then the atom names and the coordinates of the initial file will be mandatory in GROMACS. even for molecules with dummies, i can signify any atom as dummy, for after EM the coordinate of the dummy will become appropriate. am i right? or there are something i did not think of?

The position of dummy atoms will be constructed from the positions of
(at least two) real atoms. So, no, you cannot change all atoms in your
molecule into dummies. Also, you need to specify a dummy construction
type for each dummy atom.

If your molecule is not too large, you can probably create some rough
coordinates manually, and make it good using energy minimzation.


-- 
Groetjes,

Anton

* NOTE: New Affiliation, Phone & Fax numbers (below) *
 _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam   |
|(   |   )| | | De Boelelaan 1083 - 1081A HV Amsterdam - Netherlands  |
| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
|_____________|_______________________________________________________|