[gmx-users] protein embedded into membrane.
Hi, When I tried to pack different proteins around the lipids (this protein I put it in the position which was nearly going to jump out of the lipids, so it's not exactly inserted into it, just very shallow into it), I used the vmd to see the system.gro, which without being inflated first, I noticed some warnings like this: Warning) Unusual bond between residues: 40 (protein) and 491 (none) Warning) Unusual bond between residues: 40 (protein) and 491 (none) Warning) Unusual bond between residues: 40 (protein) and 491 (none) when I removed those residues such as 491 (none), not protein ones, those warning disappeared. I noticed on Justine's tutorial, there were 26 iterations of scaling down. I did those iterations step by step manually before and cost me nearly 40 mind-not-running minutes to finish, but later I spent crazy 2 hours or more to write a short and clumsy script to save mine 40 mins work in the future. This is not the point. The point was that, are there some shortcuts? I wonder whether I could avoid doing those inflategro first, and then shrink and energy minimization also being avoided by simply removed those lipids (I know I still need a final EM). or, Can we locally inflated those membrane and then locally packed them together. Very local, or maybe just simply removed those lipids. How could I make sure the removal ones are going to be nice, from which sides I should check. Thanks and best regards, lina p.s To avoid a very trivial description, I put some background information below, thanks for your time. from Tieleman's website http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis and Justine's webpage http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html I tried pack the lipids around the protein, no doubt followed perfectly based on the tutorial before. -- 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
Re: [gmx-users] protein embedded into membrane.
#ZHAO LINA# wrote: Hi, When I tried to pack different proteins around the lipids (this protein I put it in the position which was nearly going to jump out of the lipids, so it's not exactly inserted into it, just very shallow into it), I used the vmd to see the system.gro, which without being inflated first, I noticed some warnings like this: Warning) Unusual bond between residues: 40 (protein) and 491 (none) Warning) Unusual bond between residues: 40 (protein) and 491 (none) Warning) Unusual bond between residues: 40 (protein) and 491 (none) when I removed those residues such as 491 (none), not protein ones, those warning disappeared. VMD is detecting close contacts, not actual bonds, but since its heuristic algorithm tells it there are bonds, then you get these warnings. Perhaps a simple EM will resolve them, but maybe not. I noticed on Justine's tutorial, there were 26 iterations of scaling down. I did those iterations step by step manually before and cost me nearly 40 mind-not-running minutes to finish, but later I spent crazy 2 hours or more to write a short and clumsy script to save mine 40 mins work in the future. This is not the point. The point was that, are there some shortcuts? I wonder whether I could avoid doing those inflategro first, and then shrink and energy minimization also being avoided by simply removed those lipids (I know I still need a final EM). or, What is presented in the tutorial is simply one way to build a membrane protein system. If you have an easier case, then as long as you can justify your methods, do what you see fit. Perhaps the iterations of InflateGRO are, in your case, unnecessary. There is also a new tool called g_membed that might be useful. It is far more automated than InflateGRO, but I have never used it myself. Can we locally inflated those membrane and then locally packed them together. Very local, or maybe just simply removed those lipids. Not to my knowledge, unless you write this program yourself. How could I make sure the removal ones are going to be nice, from which sides I should check. I don't understand what you're asking for here. -Justin Thanks and best regards, lina p.s To avoid a very trivial description, I put some background information below, thanks for your time. from Tieleman's website http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis and Justine's webpage http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html I tried pack the lipids around the protein, no doubt followed perfectly based on the tutorial before. -- 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 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
RE: [gmx-users] protein embedded into membrane.
Thanks for your answering. I will check those further later. The unclear question was that, to the final .gro. How can I tell it that one (protein embedded in membrane) is okay or nice, so I can continue. based on area per lipids, or after EM ... are there some criteria? Thanks and best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, October 04, 2010 11:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] protein embedded into membrane. #ZHAO LINA# wrote: Hi, When I tried to pack different proteins around the lipids (this protein I put it in the position which was nearly going to jump out of the lipids, so it's not exactly inserted into it, just very shallow into it), I used the vmd to see the system.gro, which without being inflated first, I noticed some warnings like this: Warning) Unusual bond between residues: 40 (protein) and 491 (none) Warning) Unusual bond between residues: 40 (protein) and 491 (none) Warning) Unusual bond between residues: 40 (protein) and 491 (none) when I removed those residues such as 491 (none), not protein ones, those warning disappeared. VMD is detecting close contacts, not actual bonds, but since its heuristic algorithm tells it there are bonds, then you get these warnings. Perhaps a simple EM will resolve them, but maybe not. I noticed on Justine's tutorial, there were 26 iterations of scaling down. I did those iterations step by step manually before and cost me nearly 40 mind-not-running minutes to finish, but later I spent crazy 2 hours or more to write a short and clumsy script to save mine 40 mins work in the future. This is not the point. The point was that, are there some shortcuts? I wonder whether I could avoid doing those inflategro first, and then shrink and energy minimization also being avoided by simply removed those lipids (I know I still need a final EM). or, What is presented in the tutorial is simply one way to build a membrane protein system. If you have an easier case, then as long as you can justify your methods, do what you see fit. Perhaps the iterations of InflateGRO are, in your case, unnecessary. There is also a new tool called g_membed that might be useful. It is far more automated than InflateGRO, but I have never used it myself. Can we locally inflated those membrane and then locally packed them together. Very local, or maybe just simply removed those lipids. Not to my knowledge, unless you write this program yourself. How could I make sure the removal ones are going to be nice, from which sides I should check. I don't understand what you're asking for here. -Justin Thanks and best regards, lina p.s To avoid a very trivial description, I put some background information below, thanks for your time. from Tieleman's website http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis and Justine's webpage http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html I tried pack the lipids around the protein, no doubt followed perfectly based on the tutorial before. -- 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 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 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
Re: [gmx-users] protein embedded into membrane.
#ZHAO LINA# wrote: Thanks for your answering. I will check those further later. The unclear question was that, to the final .gro. How can I tell it that one (protein embedded in membrane) is okay or nice, so I can continue. based on area per lipids, or after EM ... are there some criteria? Area per lipid will equilibrate with sufficient simulation. Otherwise, use normal EM criteria to determine whether or not your system is in a reasonable configuration. -Justin Thanks and best regards, lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, October 04, 2010 11:27 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] protein embedded into membrane. #ZHAO LINA# wrote: Hi, When I tried to pack different proteins around the lipids (this protein I put it in the position which was nearly going to jump out of the lipids, so it's not exactly inserted into it, just very shallow into it), I used the vmd to see the system.gro, which without being inflated first, I noticed some warnings like this: Warning) Unusual bond between residues: 40 (protein) and 491 (none) Warning) Unusual bond between residues: 40 (protein) and 491 (none) Warning) Unusual bond between residues: 40 (protein) and 491 (none) when I removed those residues such as 491 (none), not protein ones, those warning disappeared. VMD is detecting close contacts, not actual bonds, but since its heuristic algorithm tells it there are bonds, then you get these warnings. Perhaps a simple EM will resolve them, but maybe not. I noticed on Justine's tutorial, there were 26 iterations of scaling down. I did those iterations step by step manually before and cost me nearly 40 mind-not-running minutes to finish, but later I spent crazy 2 hours or more to write a short and clumsy script to save mine 40 mins work in the future. This is not the point. The point was that, are there some shortcuts? I wonder whether I could avoid doing those inflategro first, and then shrink and energy minimization also being avoided by simply removed those lipids (I know I still need a final EM). or, What is presented in the tutorial is simply one way to build a membrane protein system. If you have an easier case, then as long as you can justify your methods, do what you see fit. Perhaps the iterations of InflateGRO are, in your case, unnecessary. There is also a new tool called g_membed that might be useful. It is far more automated than InflateGRO, but I have never used it myself. Can we locally inflated those membrane and then locally packed them together. Very local, or maybe just simply removed those lipids. Not to my knowledge, unless you write this program yourself. How could I make sure the removal ones are going to be nice, from which sides I should check. I don't understand what you're asking for here. -Justin Thanks and best regards, lina p.s To avoid a very trivial description, I put some background information below, thanks for your time. from Tieleman's website http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis and Justine's webpage http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html I tried pack the lipids around the protein, no doubt followed perfectly based on the tutorial before. -- 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 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 -- 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 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
