Hi Justin, Thanks for the quick reply. I am also following the martini tutorial in order to do the CG simulations. Here are the following steps which I am doing. Please have a look at them.
1) Cleaned the 1SU4.pdb file and renamed it to 1SU4_clean.pdb 2) converted 1SU4_clean.pdb to its CG structure using awk script and named it to 1SU4_cleancg.pdb 3) Then created the sequence of 1SU4_clean.pdb file and also the .ssd files. 4) Then using the seq2itp script created the protein.itp file for 1SU4. 5) Now I don't understand after this point what should I do because I also have to include DSPC molecules. Where should I include them I mean at which step? When I make my .top file for the protein do I include DSPC molecules there or anywhere else? Please let me know Sunny On Sun, Oct 11, 2009 at 4:30 PM, Justin A. Lemkul <[email protected]> wrote: > > > sunny mishra wrote: >> >> Hi All, >> >> I am working on the CG simulations of the proteins and lipid bilayers. >> I am confused of how to set up the whole system for simulations. I got >> the DSPC lipid bilayer from martini website and I have 1SU4.pdb file >> with me. I cleaned the .pdb file and now I want to include the 14 DSPC >> molecules in my .pdb file. I don't know if I am going in the right >> direction or not. Please let me know how to set up the simulation for >> the same if you have some idea. I will appreciate your help. >> > > I wrote a tutorial for atomistic membrane protein systems: > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html > > It may provide some useful information, since the premise for constructing > the system is the same. Our web server is currently down due to a power > outage at our University, but I should have everything up and running by > tomorrow. > > -Justin > >> Thanks, >> >> Suny >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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/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/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
