On Wednesday 13 January 2010 02:35:54 Mark Williamson wrote:
> No; the only public AMBER molecular dynamics engine that supports such
> chamber prmtops at this moment in time is PMEMD10 via bugfix 26.
> SANDER11 will support this when it is released in AMBER11.
Thank you, as you indicated my converted forcefield works with PMEMD10.
> Attempting to circumvent this CTITLE protection mechanism by hand and
> use such a prmtop file in SANDER10 or PMEMD10 will give you incorrect
> energies and forces as outlined. Essentially, I think you would end up
> with some form of a freaky Frankenstein projection of the CHARMM
> parameters on the basis of an AMBER potential.
Curiously enough I get the same potential energy for a system with the chamber
converted forcefield in PMEMD10 and its hand edited equivalent (lacking CTITLE
and all CHARMM/chamber specific parts). But then again, since I have no Urey-
Bradley-terms, no CMAP and the impropers "only" keep a ring more or less
planar, this is not so surprising.
After reading your paper on chamber I am wondering which energy statement was
used for CHARMM to give the same energy as AMBER. The statments our group
usually uses give different energies. Could you please provide a sample energy
statement or script for CHARMM as was used in the publication please.
Thank you!
Thomas Taylor
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 21 2010 - 01:00:03 PST
