On 4/16/13 1:05 PM, Albert wrote:
Hello:
I've built a system with CHARMM-GUI, and I am trying to mimize it with
following em.mdp file
title = steepest descent energy minimization
define = -DPOSRES -DPOSRES_LIG
cpp = /usr/bin/cpp
include
Hi Justin:
thanks for kind reply.
Yes, there many atom clashes in CHARMM-GUI system, so I add very
strong force on protein and ligands, and try to minimize the rest of the
system
do you have any idea how can I solve the issue and make it work?
thanks a lot
Albert
On 04/16/2013 07:09
On 4/16/13 1:13 PM, Albert wrote:
Hi Justin:
thanks for kind reply.
Yes, there many atom clashes in CHARMM-GUI system, so I add very strong force
on protein and ligands, and try to minimize the rest of the system
do you have any idea how can I solve the issue and make it work?
On 04/16/2013 07:28 PM, Justin Lemkul wrote:
Create a more physically reasonable starting structure.
-Justin
the protein and ligand are already minimized, but CHARMM-GUI create the
mix lipids automatically which I cannot change them.
ALBERT
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On 4/16/13 1:31 PM, Albert wrote:
On 04/16/2013 07:28 PM, Justin Lemkul wrote:
Create a more physically reasonable starting structure.
-Justin
the protein and ligand are already minimized, but CHARMM-GUI create the mix
lipids automatically which I cannot change them.
Then you will
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