vivek sharma wrote:
Hi All,
I want to use g_lie function of gromacs to calculate the binding free
energy og a ligand with the protein. For the same I need to run two MDS,
one for ligand only and one for ligand+protein complex (please correct
if I am wrong).
What are the checks that I should take care in this case, e.g. Do I need
to keep the same box size, or same number of solvation molecule in two
cases ?
or similar things.
And also I am unable to run the MDS for ligand only as it gives the
error like.
...Residue 'D4N' not found in residue topology database.....
You're running pdb2gmx on the structure containing the protein and the ligand,
aren't you?
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database
For the ligand+protein complex I followed the drug-enzyme tutorial by J
E Kerrigan, and it worked well.
Then you should be able to translate those same exact steps into how you should
treat your situation, alleviating the above problem.
How can I run the MDS for ligand only ?................................
If I will take the .itp from the PRODRG and use it as .top and bypass
the pdb2gmx step as mentioned in the tutorial, will it work ? (consider
the difference in two cases one is ligand only and other is
ligand+protein ).
Yes. In fact, PRODRG gives a .top, not an .itp file. The modifications are
explained in the tutorial you refer to.
Be aware that the charges and charge groups assigned by PRODRG often require
modification before they are considered satisfactory.
-Justin
Please suggest...
With Thanks,
Vivek
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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