[gmx-users] to Maik Goette about introduction of ZN in proteins.

Maik Goette mgoette at mpi-bpc.mpg.de
Thu Nov 10 14:25:40 CET 2005


No, I added them directly to the sections in the topology.
I made a python script for that, which does a neighbour search for the 
zincs in the gro-file, measures the distances/angles and includes the 
parameters in the topology file. I can send it to you, but there's, as 
usual, no guarantee.
You should also have python and several packages installed.
Right, I changed it to 0.773...this is also done by the script
Yes and No...I simply took the original (unprotonated!) CYS...The charge 
of the sulphur and (in my case) histidin is also changed by the script.

Everything was changed directly in the topology file.
You may have to insert an unprotonated CYS in the RTP- and 
HDB-file...but I'm not sure, because I never did anything with the GMX-FF.
In the AMBER-port, I use, there is an unprotonated CYS included.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

Иванов Миша wrote:
> Dear Maik,
> thank you for description of ZN-ion introduction in proteins structure:
>      "I took the mean of the distances in the crystal structure as bond length
>      and a weak force constant, which I took by intuition...:). I did the
>      same for the angles. I think, you don't have to care about the
>      dihedrals...It worked fine with no settings (so GROMACS sets 0s, when I
>      remember correctly).
>      The charge on the zinc shouldn't be 2, according to severeal papers,
>      which used that method. with a charge of around .7 it worked fine. Don't
>      forget to spread the opposing charges equally to the 4 complexing atoms,
>      to achieve a 0 total charge."
> However, I am novice in the molecular dynamics, and I want precise this outline.
> Did I understood correctly, that you:
> 1) introduced several bonds (Zn-ligand) and angles (ligand-zinc-ligand) in ffgmx.itp, where the bonded parameters are listed
> 2) changed the ZN charge to +0.7
> 3) introduced a new amino acid CYS-, possessing a negatively charged Sulfur in ffgmx.rtp, the file holding the residue database
> sincerely yours,
> Misha Ivanov   
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