Hi Justin, Thank you so much for a swift response. I will try as suggested and get back to you with my hurdles.
Appreciate the help! Best Wishes, Ankita On Thu, Aug 9, 2012 at 4:09 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/9/12 10:40 AM, Ankita naithani wrote: >> >> Hi all, >> >> I am trying to put a tetrameric protein for Energy Minimization to be >> followed by MD simulation of course. But, my problem is that it is a >> tetramer and also I need to perform the simulation with the ligand. I >> have read the tutorial for Protein-Ligand simulation but that explains >> for only one chain, whereas I am talking about 4 chains here. >> I need to put in my tetramer with ligands attached for simulations. >> If I have understood correctly, the tutorial mentions about extracting >> the ligand from PDB and then copying the PDB file of the extracted >> ligand into PRODRG and then retrieving the topology file from there >> and appending it to the topology output of the protein without ligands >> attached. But this is specific for one chain i.e. the PDB co-ordinate >> given to PRODRG is for the ligand from one chain. > > > Yes, and you would have to acquire properly processed coordinates for each > copy of the ligand. You only need one .itp file (which in theory should be > the same, regardless of which copy of the ligand you input to PRODRG), but > you need coordinate files for the four copies of the ligands from each > chain. These would then be appended to the processed protein coordinate > file in the same manner as the tutorial suggests. > > PRODRG topologies require significant modification to be considered viable > for real simulation use. See hints in the tutorial and associated > publications. > > >> The second question is that can I not submit the whole protein-ligand >> complex to GROMACS and then run pdb2gmx for generating topology. How >> do I go about that? I understand that I would have to change the top >> directories of GROMACS to accommodate my ligands but I don't know how >> to do that. >> > > Run pdb2gmx on the protein only, then append ligand coordinates as suggested > above. > > -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 > * Only plain text messages are allowed! > * 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 -- Ankita Naithani -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
