francesco oteri wrote:
The author of such work published partial charges, but nothing about
other parameters.
In order to carry out any simulation, you need more than charges. If they did
any subsequent validation of the charges, they must have assigned these
parameters. If they calculated charges and did no validation, then you should
question whether or not the charges are valid.
The force-fields used are gromos43A1 and CHARMM22. The GROMACS standard
distribution contains nothing about iron sulphur cluster.
Nonstandard additions to force fields are not included in Gromacs distributions.
-Justin
Thank you
2011/10/6 Mark Abraham <[email protected]
<mailto:[email protected]>>
On 6/10/2011 11:24 PM, francesco oteri wrote:
Dear gromacs users,
I've to simulate a protein with an 4Fe-4S and a 3Fe-4S iron
sulphur cluster.
Lot of approaches are present in literature. There are a lot of
papaers suggesting partial charges
but very few suggestions regarding bonded and not bonded parameters.
All such work should describe a source for such parameters, if they
are not in the standard force field.
So i am wondering if any member of this mailing list can send me
a link, a file or something advice can be useful to
obtain the topology of a protein with the iron sulphur clusters.
It is worth noting that I am not interested in electronic
properties so also advice using restraint are ok for me.
The authors of such work would be a good place to ask.
Mark
--
gmx-users mailing list [email protected]
<mailto:[email protected]>
http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>
Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
<http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [email protected]
<mailto:[email protected]>.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>
--
Cordiali saluti, Dr.Oteri Francesco
--
========================================
Justin A. Lemkul
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
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
