[gmx-users] H-bond in UA

Henrik Rundgren henrik at physc.su.se
Tue Mar 23 15:08:01 CET 2004

I have a question concerning the H-bond.
I haven't been able to find satisfying answers to the H-bond affect 
wilst using united-atom FF's. Some of them should explicit the polar H, 
but how well do they work?

To simulate a cyclic peptide which includes the nonconventional a.a's 
ABU, SAR, MEXXX I apparently "have" to use the UA FF. Or does anyone 
have these a.a's in their all-atom FF's?
NMR studies shows that there is several H-bondsin my peptide, how well 
would the united-atom FF take thses into account? It is essential for 
the structure that they are present.


Henrik Rundgren
Division of Physical Chemistry
Arrhenius Laboratory
Stockholm University
S-106 91 Stockholm

E-mail:    Henrik at physc.su.se
Telephone: +46-(0)8-16 12 63
Fax:       +46-(0)8-15 21 87
Website:   www.fos.su.se/~henrik

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