On 4/16/13 9:07 AM, Group Gro wrote:
Dear GROMACS users,
Hi.
I want to study different protein-drug complexes and I follow the procedure
mentioned in the
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/.
I copied and pasted the positions of each drug to the end of conf.gro and did
other steps. Is this approach true while I don't know the best place to dock
it?If not, how can I add drug without using Autodock, Gold, or other docking
softwares? Doeas each drug find the best place to dock?
The approach of copying and pasting coordinates assumes you believe that those
coordinates are a realistic representation (i.e. from docking or
crystallography). If you just place the molecule in some random way, there's no
telling if it's right. The starting position will heavily bias the outcome. If
you're not sure, invest some time in learning docking.
My next question is this: When I have different drugs and consider each complex
of them separately, what factor(s) should be my criteria to find the best drug
which has the highest effect on the protein (each drug has different nubmer of
atoms)?
I would suggest you consult the literature here and make an assessment based on
what you know about your particular protein. There is no catch-all answer.
Binding free energy may be useful, but that's just a generic answer with no
knowledge of what you're trying to do.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
