[gmx-users] Re: ligand force field parameters
mic0404 at yahoo.com
Sun Dec 14 22:25:01 CET 2003
On Fri, 12 Dec 2003, Daan van Aalten wrote:
> I would be very grateful if you could send me the ligands that did not
> work for you in the PRODRG server - it will help us improve the program
> (or, not uncommon, find the errors in your starting coordinates)
I will be happy to discuss with you the merits and
dangers of PRODRG and I will send another email with more
details to your own address. Here and for now I only want to
apologize. I might have somewhat overstated my concerns about PRODRG.
I do believe that it is a great peace of work, and it has for
a long time been over-due in the community. In particular for
people who cannot be bothered with developing their own
force-fields, i.e., for most people who do molecular simulation,
its an invaluable tool. A major drawback of other programs such
as Amber, Charmm, etc. is that, AFAIK, there is no compareable tool
for them (I do hope that this was not yet another slight against
somebody, please correct me if I am wrong there!)
Force-field development is an arduous and time-consuming task.
The advantage of PRODRG saving people most of this work
definitely outweights the risks that might be involved when
dealing with a few, mostly rather exotic materials.
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