[gmx-users] (no subject)

[Anton Feenstra]

Itamar Kass wrote:
[...]
> I saw that although the helix bundle structure kept, the 
> amino acids are not connect any more.  Using PROCHECK I found non-native 
> bond length and angles.
>   I used ffgmx_lipids force field, is it O.K.?  I also activated at the 
> grompp stage the –sort –shuffle flags, is it wrong?  Does Someone have 
> an idea of what wrong or how can I over come the problem?

You may have problems due to the effects of the -sort and/or -shuffle
options if you take the mdrun output trajectory (which is shuffled)
together with the grompp input .gro or .pdb file (which is not shuffled).
The order of the atoms will not match, so you get effectively random
positions for all your protein atoms. Use the (shuffled) grompp .tpr
file, or first un-shuffle the trajectory using the 'shuffle.ndx' (it
may be called slightly different) file that grompp probably created.


-- 
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"           |
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