Re: [Apbs-users] OPLS parameter file

[Nathan B. <ba...@bi...>]

Hello --

AFAIK, there is a possibility to read a pdb file in apbs, and an additional
> parameter file that defines the charge and vdw parameters. I was wondering
> is someone has already a file for the OPLS-AA force field.


One of the reasons we don't have van der Waals parameters for OPLS
distributed with APBS is because we currently only support Lorentz-Berthelot
mixing rules.  We need to add the geometric sigma mixing for OPLS in the
future and support switching between rules for different force fields.


> Also I was wondering how to search the mail archive in an efficient way. I
> tried the Sourceforge search function, but I always get "Time out waiting
> for response...". Isn't the list mirrored somewhere else, something like
> http://www.mail-archive.com?


The mailing lists aren't mirrored anywhere.  I think SF.net is having some
intermittent problems with their search; it's worked for me in the past but
is not working right now.  I've filed a bug with SF.net; sorry for the
inconvenience.

Thanks,

Nathan


>
> Thank you
> Marius
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-- 
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/