Faezeh Nami wrote:
For MD simulation of metalloproteins, people generally change the charge
of atoms attached to the metal center based on quantum mechanics studies.
If an .itf file shouldn’t be modified, how these changes can be made?
QM studies will also tell you that fixed charges on me
For MD simulation of metalloproteins, people generally change the charge of
atoms attached to the metal center based on quantum mechanics studies.
If an .itf file shouldn’t be modified, how these changes can be made?
Faezeh
On Fri, Jul 22, 2011 at 1:15 PM, Justin A. Lemkul wrote:
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> Faezeh N
Faezeh Nami wrote:
Dear Itamar
Thank you for the reply.
If I modify Cys parameters in the *rtp file in order to add the
Cys-label parameters, it will be applied to other Cys in the protein as
well. Isn't it?
Set the name of your modified residue to something unique (in both the input
c
Dear Itamar
Thank you for the reply.
If I modify Cys parameters in the *rtp file in order to add the Cys-label
parameters, it will be applied to other Cys in the protein as well. Isn't
it?
In case of modification of *itp file, should I modify all nr or qtot after
the Cys? What about bonds?
Best
Hi Faezeh,
You can modify the FF and add the Cys-label parameters to the *rtp and
*hdb files, such that pdb2gmx will be able to use them. Another why is
use the original pdb as a starting point and modify the output *gto,
*itp and *top files.
Just remember that in anycase, it is better to co
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