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 metal ions bound to proteins
are insufficiently accurate. If you feel that you have some justification for
what you're doing, by all means, proceed and change the charges, but you still
haven't said what .itp file you're trying to modify and in what way. My
suggestion was to leave any protein topology that pdb2gmx produces alone if it
involves adding or removing atoms or changing bonded parameters. Itamar
suggested modifying by hand the output .gro, .itp, and .top files in order to
introduce a new residue. I disagree with this recommendation as it is very
error prone and inefficient.
-Justin
Faezeh
On Fri, Jul 22, 2011 at 1:15 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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 coordinate file and the .rtp entry).
In case of modification of *itp file, should I modify all nr or
qtot after the Cys? What about bonds?
What .itp file do you want to modify? Making changes to the pdb2gmx
output is a bad idea. You'll have to change any and all subsequent
atom numbers, and that extends to all of the bonded parameters as
well, and you will have to add lots in. This procedure is very
error-prone. I would suggest building (and thoroughly checking) an
.rtp entry for your modified residue.
-Justin
Best,
Faezeh
On Thu, Jul 21, 2011 at 5:51 AM, Itamar Kass
<itamar.k...@monash.edu <mailto:itamar.k...@monash.edu>
<mailto:itamar.k...@monash.edu
<mailto:itamar.k...@monash.edu>__>> wrote:
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 copy the files
into
your local directory so an change you made will not effect other
simulations.
Cheers,
Itamar
PS I can recommend on this site which can help you in the process
http://compbio.biosci.uq.edu.__au/atb/
<http://compbio.biosci.uq.edu.au/atb/>
On 21/07/11 7:43 PM, Faezeh Nami wrote:
Dear all
I am trying to simulate a protein which a label (a small
organic
molecule) is covalently attached to a cysteine. Worth to
say there
is no label in the original pdb file of protein and it was
attached to the Cys. using a software.
Should I insert the label parameters into the conf.gro
file or I
need to modify a force field? If there is someone who has
experiences in such systems, please have some advice.
Thanks in advance,
Faezeh
--
"In theory, there is no difference between theory and
practice. But, in practice, there is." - Jan L.A. van de Snepscheut
==============================__=============
| Itamar Kass, Ph.D.
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|
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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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