[gmx-users] [Fwd: kindly help!]

David van der Spoel spoel at xray.bmc.uu.se
Wed May 18 13:13:20 CEST 2005

Respected Sir,

      Greetings in the name of the lord!'

                       With due respect i hereby require a kind help
from you regarding the Gromacs tutorials. In my protein I have a
Calcium ion Ca2+, which is not accepted by the gromacs. I know that
this doesn't consider the heteroatoms. I have deleted all the
heteroatoms, except the Ca2+, as it in present in the active site on
the protein, which I am using and it's involved in the interaction
with inhibitors while docking. That's why I need to run Gromacs along
with the Ca2+. Could you please let me know how to include this Ca2+,
in the atom type parameter file in simple steps? Please do let me know
to which file should I make the changes to add that Ca2+, and how to
make the changes to add that, and what will be the other changes that
I have to do along with that, what are the mandatory steps to be
included to do that.  Actually I have to run minimization for my
protein, but I am not able to do so because of the presence of the
Ca2+, but I was able to run the same if I delete the Ca2+ from the PDB
file. Please do mail me in detail about the steps to be taken to run
minimization for such protein, if an unidentified atom is present in
the protein in simple steps. I have gone through the Gromacs tutorials
Chapter 5 regarding this problem, but I was not able to figure out the
solution in a better way. What to do? Please guide me.

Also if I have an inhibitor modeled by me with all the required PDB
parameters for that inhibitor, that is the coordinates of each atoms
present in it. But the atoms are not present in the topology file of
gromacs. How to add such atoms into library so that I can run the
minimization for my inhibitor? I am doing docking studies using
INSIGHTII software. For carrying out the minimization in polar
environment I have planned to use Gromacs. Kindly please help me to
carry out my work with your able guidance.

Looking forward to get a reply from you soon!

With regards,
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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