Dear Justin, Many thanks for your comprehensive mail. I will try to do it and let you know if i come across any problem..(Definetely i may bug u again :)) Thank you so much. Best regards Padhu
> > > pa...@ncbs.res.in wrote: >> Dear All, >> I'm a new comer to gromacs. I need to perform molecular dynamics >> simulation of my protein within the POPC membrane. I have downloaded the >> 128a popc lipid from Prof.Tieleman's group along with the required >> popc.itp. My protein of interest is 458 residues. Since the 128a popc is >> already Simulated for 1600 ps, i haven't done membrane only simulation. >> So >> i directly aligned my protein with the membrane using VMD and have saved >> the coordinates. However after i aligned my protein with the membrane, i >> felt the membrane was not big enough for my protein of interest, also, >> the >> N-terminal region and the loop regions in the C-terminal region and >> stretching outside water molecule above and below respectively.ow, i >> have >> two questions here... > > Yep, if the protein is sticking "out" of the box on both sides, the box is > too > small. > >> 1. How would i increase the number of lipids from the existing one? > > Two options: > > 1. genconf -nbox will give integer multiples of the lipid system (i.e., > -nbox 2 > 2 1 will expand the bilayer in the x and y directions and give 512 lipids) > > 2. genbox -cs popc128a.pdb -box (whatever dimensions) allows you a bit > finer > control over how large the box is and how many lipids will result. > >> 2. Also, i should increase increase the number of water molecules above >> and below the membrane so that it covers the whole region of N-terminal >> and also the loop regions of the C-terminal. > > Expand the box using editconf and add solvent with genbox. > >> Now, How to perform these tasks??If i do so will it be compatible with >> the >> popc.itp file which i downloaded from the Prof. Tieleman's group? >> > > None of the above operations have any influence on the parameters > contained in > popc.itp. If you are unsure about Gromacs workflows, file formats, etc. > then > you really need read the manual and do some more basic tutorial material > before > you attempt a difficult simulation like a membrane protein. There are a > lot of > pitfalls in simulating such a complex system, and if you are not ready for > them, > then you can waste a whole lot of time generating nonsensical results :) > >> 3. My third question is while aligning my protein with the membrane >> should >> i make a hole first or after aligning the protein should i remove the >> overlapping lipids with the proteins?which one would be better?? >> > > There are several methods for doing this. See below. > >> I have tried out some of the methodologies available in the internet but >> it dosen't help me.If anyone of you have a detailed step by step >> methodology right from the first step to till running the MD simulation >> please let me know. > > Saying you've tried things and they didn't work is useless. What did you > try? > What links can you provide? Have you tried the membrane protein tutorial > linked > from the Gromacs site? That's about as step-by-step as it gets. > > -Justin > >> Your help will be highly appreciated. >> Looking forward to hear from you. >> >> Best regards >> Padmanabhan >> > > -- > ======================================== > > 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/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/mailing_lists/users.php > -- 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/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/mailing_lists/users.php