pkmukher wrote:
Dr Spoel,
Thanks for your suggestions. Actually i would be using the
GROMOS96 force field(option 0 in pdb2gmx GROMOS96 43a1).I am
new to the GROMACS package.I wish to simulate a
ligand-protein system and had been using the drug-enzyme
tutorial available for this purpose. In the tutorial they
use the PRODRG2 server to generate the ligand structure
files. I find that the charges were calculated for a
structure with only polar hydrogens present. This is then
used to form the ligand-protein complex and solvation,
neutralization etc.I was wondering
1) which ligand file should i use to generate my gaussian
inputs. one with all the hydrogens or one with just the
polar hydrogens.
Well the latter won't get you very far.
2) I presume that for the gaussian calculation I have to
submit an all hydrogen structure. In that case how do I
refit the charges onto the polar hydrogen only structure
which i will use for the generataion of the ligand-protein
complex(as per the tutorial)
Not a simple question. Force field extension is a dark art and very easy
to do badly. You can search the mailing list for advice people have
given before on this topic, but it's mostly been me and Tsjerk, and we
mostly tell people they are crazy to start their MD experience
parameterizing an extension for a force field. That doesn't seem to stem
the flow of (under)graduate students being set tasks that are likely to
be beyond their capacity to do without expert supervision - and if they
had that they wouldn't need to ask basic questions about parametrization
on a mailing list. Nonetheless, you must read up on how the rest of the
force field was developed in order to come up with an even vaguely
reasonable strategy for extending it.
3) Do you think that the current forcefield is good for
simulation of ligand-protein complexes.
You should find some relevant literature and read it yourself :-)
Mark
_______________________________________________
gmx-users mailing list [EMAIL PROTECTED]
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
