Dear Raffaella,
> I would like to simulate an organic molecule (an alcohol) in water. I
> have been reading the manual (amber 8) to understand how to build the
> force field for a simple alcohol (or to use what is already in the
> distribution). However I am not getting very far in
> understanding how to
> do it (meaning how to build the residue and the parameter file).
I would try taking a look at the tutorials at:
http://www.rosswalker.co.uk/tutorials/amber_workshop/
Particularly tutorials 4 and 5.
These will take you through step by step creating prmtop files for
non-standard residues and will show you both the manual and antechamber
approaches...
All the best
Ross
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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Received on Fri Apr 07 2006 - 17:17:59 PDT
