Hi Gmxions, The value Kb = 1673.6 KJ/mol nm2 working good for restraining distance (type6, Harmonic potential) between Fe(II) and corresponding ligating atoms N and O (of amino acids) at the end of 5000 steps of energy minimization. That is newly introduced Kb value is able to restraint at around 2-3 A (Which is the average value found from crystal structure) when comparing to more than 5A in the absence of Kb value.
I am going to start MD with a hope that this success will also be there at the end of 2ns simulation Is there any second thought? With thanks! B.Nataraj On Wed, 10 May 2006 05:16:26 -0700, "raja" <[EMAIL PROTECTED]> said: > Hi Mr Tsjerkw, > Thanks for your mail. Infact I intented to attach > the reference link but I missed it. Anyway here is the link where I > taken > the value of Kb. Infact the reference only talk between Fe and O atoms. > I belive this value will be more reasonably for my purpose. I will > update the outcome of the result of MD using this restraints after my > work completes. > > In mean time here is the reference link " > http://www.jbc.org/cgi/content/full/280/51/42188 " > > For quick find out on the page , use this key work "force constant of > 4.0 kcal/mol/Å2" and please let me know the validity of my judgement. > > With Thanks ! > B.Nataraj > > > > On Wed, 10 May 2006 13:50:17 +0200, "Tsjerk Wassenaar" > <[EMAIL PROTECTED]> said: > > Hi Raja, > > > > No objections from my side. But if you could also include the > > references resulting from your literature study, that would be nice to > > have in the archive (may save somebody searching the literature to > > find some iron - ligand parameters). > > > > Cheers, > > > > Tsjerk > > > > On 5/10/06, raja <[EMAIL PROTECTED]> wrote: > > > > > > Hi gmxions, Based on the litterature search , I am going to use Kb > > > value of " 4 Kcal/mol A2" (1673.6 KJ/mol nm2)as harmonic bonded > > > force field constant(type 6) for restraining distance of Fe(II) > > > ligated with atoms of 2 Nitrogen and 1 Oxygen. If any one having > > > objection please correct me ): . > > > > > > > > > With thanks ! > > > B.Nataraj > > > -- > > > raja [EMAIL PROTECTED] > > > > > > -- > > > http://www.fastmail.fm - Send your email first class > > > > > > _______________________________________________ > > > gmx-users mailing list [email protected] > > > http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php > > > > > > > > > > > -- > > > > Tsjerk A. Wassenaar, M.Sc. Groningen Biomolecular Sciences and > > Biotechnology Institute (GBB) Dept. of Biophysical Chemistry > > University of Groningen Nijenborgh 4 9747AG Groningen, The Netherlands > > +31 50 363 4336 > -- > raja > [EMAIL PROTECTED] > > -- > http://www.fastmail.fm - A no graphics, no pop-ups email service > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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/mailing_lists/users.php -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - And now for something completely different _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
