Hi all,
I have a question concerning the H-bond. I am running a protein-peptide
simulation in water.
My starting structure is a X-ray complex. What I am observing is that after 200ps an important
hydrogen bond between the peptide and the protein is breaking (ARG -- ASP). Now, since experimental
data and previous MD (using CHARMM as ff) have demonstrated that this hydrogen bond is very
important for the interaction, I am concluding that in my case I have a problem with my used ffG43a1.
I have been reading few papers and I see that CHARMM ff uses an explicit hydrogen-bond contribution
in the calculation. From the gromacs manual there is not note about it. In order to validate my
assumption, I am thinking either to swap to ffopls or to perform a small dynamics at low temperature
and increase it to 300K to allow a better equilibrium.
Any suggestion are very welcome.
Regards
thanks
andrea
--
-------------------------------
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
-------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
