Dear Justin, I have 6 EDO and 1 TRS ligans. I created coordinate and .itp files for each EDO molecule using prodrg web server. I am adding coordinates of each EDO molecule into a file called conf.gro. The conf.gro file is obtained from without_EDO_TRS. pdb ( there is not ligands). is this procedure correct?
I do not know what to do about EDO.itp because .itp files obtained from the prodrg web server are the same. How can I create one .itp file for all the EDO molecules? Thanks 16 Nisan 2011 02:08 tarihinde Justin A. Lemkul <[email protected]> yazdı: > > > ahmet yıldırım wrote: > >> Dear users, >> >> Is there anyone has a tutorial of the ligand have more than one molecules? >> > > Perhaps you can describe in more detail what it is you hope to accomplish. > The procedure for dealing with multiple ligands is, in principle, no > different from a single ligand. There are not tutorials available for every > variation of a procedure. > > -Justin > > > For example: >> *_topol.top:_* >> [ molecules ] >> ; Compound #mols >> Protein_chain_A 1 >> Protein_chain_B 1 >> *ligandname * 3 >> >> Thanks in advance >> -- >> Ahmet YILDIRIM >> >> > -- > ======================================== > > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM
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