> I am just starting with amber7. When i generated my first parameter
> files, i made disulfide bonds with the unit editor, just
> drawing them.
> Talking with colleagues i learned that they all make disulfide bonds
> with the bond command. I'd like to know if it okay to draw disulfide
> bonds in the unit editor or if it is better to make them via bond.
The two methods should accomplish exactly the same thing. Thus if you prefer
to draw the bonds in by all means do that. Just bare in mind however that if
you have a very large system drawing in the disulphide bonds may be
unwieldy. It also stops you scripting the creation of prmtop and inpcrd
files which would prevent you from building several variations on the same
system very quickly. You should ideally make sure you know how to use both
methods.
All the best
Ross
/\
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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Received on Wed Aug 31 2005 - 18:53:01 PDT
