[gmx-users] Re: ligand force field parameters

[m b]

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)

Dear Daan,
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.
best wishes,
Michael



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