Re: [gmx-users] Which POPC Bilayer to start?
I've had success with Tieleman's lipids. I used popc128b.pdb. Since it has the extra ns of equilibration, I figured it would cause fewer problems. However, once you start messing around with making hole in the membrane and adding a protein, you'll need to re-equilibrate again (EM PR).JimOn Sep 20, 2006, at 5:48 PM, Akshay Patny wrote:Hi AllI am trying to use POPC bilayer for doing GPCR simulation.I have come across two options of generating a POPC bilayer 1. I can generate a POPC bilayer from the VMD Membrane plug-in, wherein themembrane is generated from the pre-built membrane square patches and lipidtails are (almost) fully extended.2. Alternatively, I can download the pre-equilibrated POPC bilayer from Dr.Tieleman's website, http://moose.bio.ucalgary.ca/index.php?page=PeopleSince, I am new to the GPCR-membrane modeling, can you suggest me which outof the above two options can be a better starting point for the simulationof my GPCR protein? A membrane generated from VMD or a pre-equilibratedmembrane?? Would the equilibration time for my protein be lesser in one outof the two?If option 2 is a good idea then out of popc128a.pdb and popc128b.pdb (bothavailable from Prof. Tieleman's website), which will be a better model tostart with?Thank you very much in advance.AkshayAkshay PatnyGraduate Research AssistantFaser Hall 417, Department of Medicinal ChemistryResearch Institute of Pharmaceutical SciencesUniversity of MississippiUniversity, MS 38677E-mail: [EMAIL PROTECTED]Tel: 662-915-1286 (office); Web: www.olemiss.edu___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Which POPC Bilayer to start?
Hi All I am trying to use POPC bilayer for doing GPCR simulation. I have come across two options of generating a POPC bilayer 1. I can generate a POPC bilayer from the VMD Membrane plug-in, wherein the membrane is generated from the pre-built membrane square patches and lipid tails are (almost) fully extended. 2. Alternatively, I can download the pre-equilibrated POPC bilayer from Dr. Tieleman's website, http://moose.bio.ucalgary.ca/index.php?page=People Since, I am new to the GPCR-membrane modeling, can you suggest me which out of the above two options can be a better starting point for the simulation of my GPCR protein? A membrane generated from VMD or a pre-equilibrated membrane?? Would the equilibration time for my protein be lesser in one out of the two? If option 2 is a good idea then out of popc128a.pdb and popc128b.pdb (both available from Prof. Tieleman's website), which will be a better model to start with? Thank you very much in advance. Akshay Akshay Patny Graduate Research Assistant Faser Hall 417, Department of Medicinal Chemistry Research Institute of Pharmaceutical Sciences University of Mississippi University, MS 38677 E-mail: [EMAIL PROTECTED] Tel: 662-915-1286 (office); Web: www.olemiss.edu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] Which POPC Bilayer to start?
Hi All I am trying to use POPC bilayer for doing GPCR simulation. I have come across two options of generating a POPC bilayer 1. I can generate a POPC bilayer from the VMD Membrane plug-in, wherein the membrane is generated from the pre-built membrane square patches and lipid tails are (almost) fully extended. 2. Alternatively, I can download the pre-equilibrated POPC bilayer from Dr. Tieleman's website, http://moose.bio.ucalgary.ca/index.php?page=People Since, I am new to the GPCR-membrane modeling, can you suggest me which out of the above two options can be a better starting point for the simulation of my GPCR protein? A membrane generated from VMD or a pre-equilibrated membrane?? Would the equilibration time for my protein be lesser in one out of the two? If option 2 is a good idea then out of popc128a.pdb and popc128b.pdb (both available from Prof. Tieleman's website), which will be a better model to start with? Thank you very much in advance. Akshay Akshay Patny Graduate Research Assistant Faser Hall 417, Department of Medicinal Chemistry Research Institute of Pharmaceutical Sciences University of Mississippi University, MS 38677 E-mail: [EMAIL PROTECTED] Tel: 662-915-1286 (office); Web: www.olemiss.edu ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
