[gmx-users] lipid-protein simulation
Dear all, To simulate a lipid-protein system, I'm using CHARMM36 FF and popc lipid bilayer. So I need to put popc.pdb, popc.itp and lipid.itp files in my working directory. I'm wondering: 1.if it is correct to use popc.itp generated from 50 ns-simulated popc in water? 2. I need to have lipid.itp defined by C36 FF. Would it be correct to get an individual popc.pdb and generate lipid.itp by pdb2gmx? I'm not sure about this way of generating lipid.itp, so please give me your suggestions. Would you please help me? Thanks in advance. Sincerely, Shima -- 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] lipid-protein simulation
On 9/16/12 12:34 PM, Shima Arasteh wrote: Dear all, To simulate a lipid-protein system, I'm using CHARMM36 FF and popc lipid bilayer. So I need to put popc.pdb, popc.itp and lipid.itp files in my working directory. I'm wondering: 1.if it is correct to use popc.itp generated from 50 ns-simulated popc in water? I will assume you mean the coordinate file is from a 50-ns simulation? Topologies are not time-dependent. If you can demonstrate that your membrane is properly equilibrated in this time frame, then yes, it is a plausible starting model. 2. I need to have lipid.itp defined by C36 FF. Would it be correct to get an individual popc.pdb and generate lipid.itp by pdb2gmx? I'm not sure about this way of generating lipid.itp, so please give me your suggestions. If you already have popc.itp then you don't need to run pdb2gmx. What is lipid.itp? If you're somehow thinking you need the Berger lipid parameters from Peter Tieleman, you don't. CHARMM36 was built to handle lipids, so all necessary atom types, nonbonded, and bonded parameters should already be present in the force field, thus requiring no external modification. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] lipid-protein simulation
Thanks. Yes, I want to use the coordinate file from 50-ns simulation. Would you please let me know what the criterion for knowing that the equilibrated system is proper for insertion of protein? Do the temperature, RMSD, pressure and visualization of popc-water system make me decide that it is a proper system or not? Thanks for your suggestions dear Justin. Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, September 16, 2012 9:08 PM Subject: Re: [gmx-users] lipid-protein simulation On 9/16/12 12:34 PM, Shima Arasteh wrote: Dear all, To simulate a lipid-protein system, I'm using CHARMM36 FF and popc lipid bilayer. So I need to put popc.pdb, popc.itp and lipid.itp files in my working directory. I'm wondering: 1.if it is correct to use popc.itp generated from 50 ns-simulated popc in water? I will assume you mean the coordinate file is from a 50-ns simulation? Topologies are not time-dependent. If you can demonstrate that your membrane is properly equilibrated in this time frame, then yes, it is a plausible starting model. 2. I need to have lipid.itp defined by C36 FF. Would it be correct to get an individual popc.pdb and generate lipid.itp by pdb2gmx? I'm not sure about this way of generating lipid.itp, so please give me your suggestions. If you already have popc.itp then you don't need to run pdb2gmx. What is lipid.itp? If you're somehow thinking you need the Berger lipid parameters from Peter Tieleman, you don't. CHARMM36 was built to handle lipids, so all necessary atom types, nonbonded, and bonded parameters should already be present in the force field, thus requiring no external modification. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] lipid-protein simulation
On 9/16/12 12:48 PM, Shima Arasteh wrote: Thanks. Yes, I want to use the coordinate file from 50-ns simulation. Would you please let me know what the criterion for knowing that the equilibrated system is proper for insertion of protein? Do the temperature, RMSD, pressure and visualization of popc-water system make me decide that it is a proper system or not? None of those criteria are specific enough, in my opinion. Lipid-specific metrics like area per lipid, membrane thickness, lateral diffusion, etc should all be considered. There is a wealth of literature that exists about membrane simulations from which you can draw ideas. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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] Lipid-protein simulation....
Hi Gromacs Friends, I completed Justin-Lipid Tutorial. I plan to simulate protein-lipid system to study protein-lipid interaction. My Query is like 1. I plan to use DPPC (128) lipid from Tieleman Website. I removed its periodicity as per tutorial instruction.. I found that I need the z box Dimension more than 6.59650. ( I not Change x-y box Dimension , As it affect the equilibrated DPPC layer). So with help of editconf command I changed the Z box Dimension to 8.00 while x and y are same . Is these process is right or any good suggestion in my work-flow ??? 2. I wish to put lipid membrane away from protein ( Protein is not embedded in lipid ). Should I use InflateGro?? Should I use Strong position restrain during Energy minimisation??? please give me valuable Guidance With Best Wishes and regards Rama -- 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] Lipid-protein simulation....
On 6/26/12 12:02 PM, rama david wrote: Hi Gromacs Friends, I completed Justin-Lipid Tutorial. I plan to simulate protein-lipid system to study protein-lipid interaction. My Query is like 1. I plan to use DPPC (128) lipid from Tieleman Website. I removed its periodicity as per tutorial instruction.. I found that I need the z box Dimension more than 6.59650. ( I not Change x-y box Dimension , As it affect the equilibrated DPPC layer). So with help of editconf command I changed the Z box Dimension to 8.00 while x and y are same . Is these process is right or any good suggestion in my work-flow ??? Changing the box dimensions to accommodate new species is fine. By default, if you haven't used the -center option of editconf, the coordinates are position such that the solute is centered within the box. This may or may not be what you want. Check out the workflow and tips suggested here: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/03_tricks.html 2. I wish to put lipid membrane away from protein ( Protein is not embedded in lipid ). Should I use InflateGro?? Should I use Strong position restrain during Energy minimisation??? The purpose of InflateGRO is to pack lipids around a protein. If you don't need to embed the protein in the membrane, there is no point to using InflateGRO, or programs like g_membed. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
