Hi XAvier, Thanks for your opinion. This is my maiden attempt to simulate a protein so the reason for the mistake. If possible could you please refer me some paper, which describe the simulation of a system, contains Fe (II) at its active site. I tried my best, but could not find a one.
By, B.Nataraj On Sat, 29 Jul 2006 13:34:37 +0200, "X.Periole" <[EMAIL PROTECTED]> said: > > During the simulation of protein with Fe (II) ligating > >with 2 His and 1 > > Asp residues at active site, I set every thing right > >including Kb value > > but failed to deprotonate NE2 atoms of 2 His residues > >ligating that > >Fe(II). > > What do you mean by failed ? This should not be a problem. > You can choose the protonation state of a his ... check > the ffXXX.rtp file. > > > After 2ns simulation run, the average pdb > >structure shows that > > the flip of His ring out from Fe (II), but the > >Asp-oxygen moved much > > closer to Fe (II) than its original position. If I > >compute RMSF for Fe > > (II), showing value of "0" through out the simulation > >run. The RMSF "0" > > indicates Fe (II) originally retained in its position, > > 0 fluctuations at all !!! You fixed its position or > something ? That does not seems right !! > > >but the ligating > > His flipped and Asp as a single residue held the Fe (II) > >at its original > > position. So now please tell me whether this simulation > >is valid? > > The simulation that you discribe does not seem to be > a good representation of your system ... > > XAvier > _______________________________________________ > 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 - Or how I learned to stop worrying and love email again _______________________________________________ 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
