AMBER Archive (2009)

Subject: [AMBER] GB and Atom Type

From: Alexander Seifert (alexander.seifert_at_itb.uni-stuttgart.de)
Date: Wed Nov 18 2009 - 02:58:32 CST

Dear all,

 

I am trying to run an implicit solvent MD simulation on a protein that
contains a heme iron taking into account the hydrophobic effect of the
protein surface. I read a request on the AMBER mailing list concerning
missing parameters (http://archive.ambermd.org/200401/0083.html) and David's
reply (http://archive.ambermd.org/200401/0089.html). I have the same problem
with the missing heme parameters and to be honest I don't really get how the
parameters are defined in the mdread.f file or what the values stand for.
Does anyone has suggestions how I get the missing iron parameters or is
there a way to exclude the heme from the hydrophobic effect calculation,
since it is located in the interior of the protein and therefore shouldn't
have any effect on the protein's surface interactions. I appreciate your
efforts.

 

Best regards,

 

Alexander

 

 

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber