Peter C. Lai wrote:
In this case,
Can't you just use pdb2gmx to regenerate the topology file from the merged
gro which will resolve the separate moleculechains for you?
Only if you really feel like re-writing the ligand topology from scratch as an
.rtp entry to be processed by pdb2gmx, and then attempt to make a merged
moleculetype. In short, yes, it's possible to treat a protein-ligand complex as
a single entity, but it's probably not worth the effort when it is far simpler
to #include a ligand topology and #include a position restraint file for it.
This approach also provides considerably more flexibility in terms of
restraining the protein and ligand independently, which may be required for
various applications.
-Justin
On 2011-03-30 04:25:34AM -0500, Mark Abraham wrote:
On 30/03/2011 8:14 PM, Ghassen Hassani wrote:
Dear Friends,
Right now i am working on the docking of a small ligand to a receptor. in order
to begin md simulations in gromacs, i need to create some files..
I have already docked my ligand to the receptor and i have those files:
- ligand_receptor.gro
- posre.itp (for only the receptor !!)
I have 2 Questions:
1- How can i expand the posre.itp file to also include the ligand.data ?
Don't. The position restraints file is intended to be #included from within a
[moleculetype]. You have two, so you need two position restraint files, each
#included from a different, appropriate place. The GROMACS tool genrestr can
help generate that for the ligand.
that means how can i do to create a posre.itp-file for my
ligand_receptor-komplex ?
Don't.
2- I have 2 separate top-files: ligand.top (from the prodrg-server) and the receptor.top
file. How can i "merge" the 2 files and obtain the file ligand_receptor.top for
the whole ligand-receptor-komplex ?
You need to convert one of your [moleculetype] definitions in one of your .top
files into an .itp file
(http://www.gromacs.org/Documentation/File_Formats/.itp_File) and #include it
suitably from the other. See chapter 5 of the manual for details. This is
tricky, do your homework first. Note that you should take note of the warning
here: http://www.gromacs.org/Downloads/Related_Software/PRODRG
Many thanx, please email-me on my adress:
greendreams1...@yahoo.de<mailto:greendreams1...@yahoo.de>
Yours.
No, that is against accepted netiquette. If your question is worth answering,
then that answer is worth broadcasting and archiving so others can learn from
it.
Mark
--
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
