[gmx-users] urgent question

Ran Friedman r.friedman at bioc.uzh.ch
Wed Apr 23 14:29:57 CEST 2008


You probably didn't find it because it's not so popular for simulations.
My suggestion is to look very carefully in the literature. Transition
metals are difficult to models, especially when you need to take into
account both their interactions with water and with proteins - see e.g.:

author = "Project, E and Nachliel, E and Gutman, M",
title = {Parameterization of Ca+2-protein interactions for molecular dynamics simulations},
abstract = {Molecular dynamics simulations of Ca+2 ions near protein were performed with three force fields: GROMOS96, OPLS-AA, and CHARMM22. The simulations reveal major, force-field dependent, inconsistencies in the interaction between the Ca+2 ions with the protein. The variations are attributed to the nonbonded parameterizations of the Ca+2-carboxylates interactions. The simulations results were compared to experimental data, using the Ca+2-HCOO- equilibrium as a model. The OPLS-AA force field grossly overestimates the binding affinity of the Ca+2 ions to the carboxylate whereas the GROMOS96 and CHARMM22 force fields underestimate the stability of the complex. Optimization of the Lennard-Jones parameters for the Ca+2-carboxylate interactions were carried out, yielding new parameters which reproduce experimental data.},
journal = "J Comput Chem",
year = "2008",
volume = "29",
number = "7",
pages = "1163-1169",
month = "May",
pmid = "18074346",
url = "http://www.hubmed.org/display.cgi?uids=18074346",
doi = "10.1002/jcc.20876"


Prettl Zsolt wrote:
> Hello!
> I would like to use Cr3+ for my molecule modelling but I just could
> not find a suitable one for Gromacs anywhere. If somebody has any
> suggestion, from when can I download it, please write me ASAP, because
> it is very-very important!!!!
> Thanks in advance,
> Zsolt
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080423/706451ab/attachment.html>

More information about the gromacs.org_gmx-users mailing list