[gmx-users] Re: problem in g_membed
Thank you both of you (Justin and Albert) sir. Initially I was using dppc128 and now I changed to POPE 340 and still my protein (its a GPCR protein) protrude out of the membrane (the same region; two amino acids). since you (Justin) you have mentioned that the protein must be completely inside the membrane to avoid any instability, what must I do to avoid this problem? is something wrong with my protein? The region protruding out is a loop. is it still a problem? the protein's box size is 4.49101 4.74797 7.29103 (from protein.gro). Kindly help. -- View this message in context: http://gromacs.5086.x6.nabble.com/problem-in-g-membed-tp5009503p5010166.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
[gmx-users] Re: problem in g_membed
sir, the reason for selecting POPE doesn't have much valid reason. I mean, I have referred previous works and in the recent work they have used POPE membrane for my protein (the exact protein) simulation. I have searched literature on selecting a membrane for simulation to know/understand why they have selected the particular membrane. But couldn't find put the reason why?. And, sorry I have misunderstood what you have mentioned about the protein out of the box. I get the point now. I have used editconf and have increased the Z dimension of the box. Now the protein fits inside the box and no protruding. Thank you sir. -- View this message in context: http://gromacs.5086.x6.nabble.com/problem-in-g-membed-tp5009503p5010176.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
[gmx-users] Re: problem in g_membed
I would have made a blunder by selecting the POPE membrane. But, that paper (one which used POPE for human protein) was published in ACS-Journal of Chemical Information and Modeling. I thought following high standard papers are trust worthy. Thank you so much sir. I will start learning the basics before continuing the simulation. -- View this message in context: http://gromacs.5086.x6.nabble.com/problem-in-g-membed-tp5009503p5010184.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
[gmx-users] Re: problem in g_membed
Thank you so much sir. the entire thread was highly useful. -- View this message in context: http://gromacs.5086.x6.nabble.com/problem-in-g-membed-tp5009503p5010188.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
[gmx-users] Re: Simulating a semi-membrane protein
Sir, I'm new to simulation. is there any papers or materials (book or website) to learn about the forcefields and their limitations. All the advice I get from people is to select a ff and membrane based on the previous works on that protein or protein family. I know its too much to ask but, can you please suggest some papers/materials on forcefields and selecting a membrane. I'm sure it will be useful to many beginners like me. Thankyou. -- View this message in context: http://gromacs.5086.x6.nabble.com/Simulating-a-semi-membrane-protein-tp5010032p5010050.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
[gmx-users] Re: Simulating a semi-membrane protein
Thank you both of you for taking time to help me.. This would be definitely useful. thank you so much. -- View this message in context: http://gromacs.5086.x6.nabble.com/Simulating-a-semi-membrane-protein-tp5010032p5010063.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
[gmx-users] Simulating a semi-membrane protein
Dear Users, I'm not sure if the term I coined as semi-membrane protein is correct. But My protein is half (alpha subunit) in membrane and other half (beta subunit) outside the cell. is it possible to simulate such proteins? if So, how can we use membrane for just one half? Sorry if the question is stupid. just wondering... -- View this message in context: http://gromacs.5086.x6.nabble.com/Simulating-a-semi-membrane-protein-tp5010032.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
[gmx-users] Re: Simulating a semi-membrane protein
Dear Sir, Thank you. I understand it now. But, when apply the force field, should I select the membrane ff like gromos56 (like in your KALP tutorial) or will it be a complex process to select a ff? -- View this message in context: http://gromacs.5086.x6.nabble.com/Simulating-a-semi-membrane-protein-tp5010032p5010035.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
[gmx-users] Re: Simulating a semi-membrane protein
Dear Sir, Thank you. I understand it now. But, when apply the force field, should I select the membrane ff like gromos56 (like in your KALP tutorial) or will it be a complex process to select a ff? -- View this message in context: http://gromacs.5086.x6.nabble.com/Simulating-a-semi-membrane-protein-tp5010032p5010036.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
[gmx-users] Re: problem in g_membed
Dear Sir, Thanks so much.. now what's the solution? Should I increase the box size? Already I have centered the protein and fixed the POPE membrane size. Can you tell me how to increase the box size? or is there any other solution? -- View this message in context: http://gromacs.5086.x6.nabble.com/problem-in-g-membed-tp5009503p5009632.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-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
