Re: [gmx-users] Membrane simulation with OPLS ff.
On 26 Sep, 2013, at 19:50, Justin Lemkul wrote: On 9/26/13 10:47 PM, Christopher Neale wrote: Dear Karthi: As far as I am aware, there is no OPLSAA lipid force field. I have used Berger lipids with OPLSAA protein ( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing a UA lipid with an AA protein so be aware of possible problems arising out of that. There are OPLS-compatible lipids, though they are UA, but specifically designed to be used with OPLS-AA: dx.doi.org/10.1021/ct900086b I have not seen these parameters used very widely, though. I have used the Ulmschneider lipids quite a bit and they are working well for me. You can obtain them from Lipidbook, http://lipidbook.bioch.ox.ac.uk/ , in the browser http://lipidbook.bioch.ox.ac.uk/package/ select OPLS and Gromacs. Specifically, POPC is http://lipidbook.bioch.ox.ac.uk/package/show/id/52.html Oliver -- Oliver Beckstein * oliver.beckst...@asu.edu http://becksteinlab.physics.asu.edu/ Arizona State University Department of Physics Tempe, AZ 85287-1504 USA Office: PSF 348 Phone: +1 (480) 727-9765 FAX: +1 (480) 965-4669 Department of Physics: http://physics.asu.edu/home/people/faculty/oliver-beckstein Center for Biological Physics: http://biophysics.asu.edu/CBP/person.php?ID=343 -- 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] Membrane simulation with OPLS ff.
Thanks Justin. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin Lemkul Sent: Thursday, September 26, 2013 7:51 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Membrane simulation with OPLS ff. On 9/26/13 10:47 PM, Christopher Neale wrote: Dear Karthi: As far as I am aware, there is no OPLSAA lipid force field. I have used Berger lipids with OPLSAA protein ( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing a UA lipid with an AA protein so be aware of possible problems arising out of that. There are OPLS-compatible lipids, though they are UA, but specifically designed to be used with OPLS-AA: dx.doi.org/10.1021/ct900086b I have not seen these parameters used very widely, though. Charmm has proteins and lipids, but charmm lipids require charmm tip3p water (or at least tip4p or spc, certainly not regular tip3p) and are thus slower to simulate in gromacs. I'm more recently using the Slipids (stockholm lipids) and Amber99SB-ILDN protein forcefield. Solid choices. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Membrane simulation with OPLS ff.
On 9/26/13 10:47 PM, Christopher Neale wrote: Dear Karthi: As far as I am aware, there is no OPLSAA lipid force field. I have used Berger lipids with OPLSAA protein ( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing a UA lipid with an AA protein so be aware of possible problems arising out of that. There are OPLS-compatible lipids, though they are UA, but specifically designed to be used with OPLS-AA: dx.doi.org/10.1021/ct900086b I have not seen these parameters used very widely, though. Charmm has proteins and lipids, but charmm lipids require charmm tip3p water (or at least tip4p or spc, certainly not regular tip3p) and are thus slower to simulate in gromacs. I'm more recently using the Slipids (stockholm lipids) and Amber99SB-ILDN protein forcefield. Solid choices. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Membrane Simulation
On 4/18/13 10:59 AM, Giuseppe wrote: Dear all I'm trying to start a simulation with a protein embedded in a bilayer of POPC molecules, but I have some problems when I pack the lipids around the protein. Infact I place the protein in the proper position using the editconf tool with the “-rotate” and “-center” options on, but when I scale the lipid positions with the perl script (before the energy minimization), the protein moves up, de facto off from the membrane! Obviously I've set very strong position-restraining force on protein, but it moves the same. Probably the problem is trivial, but I can't see it, so any help is much appreciated. You probably haven't set up the protein's location in a box with the same dimensions as the membrane, so it's centered within some different unit cell. -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] Membrane simulation - error during EM after inflation step
On 2/4/13 11:09 PM, John K wrote: Hello Justin, Thank you for providing a tutorial for membrane simulation. I am doing membrane simulation by following your tutorial. When I tried to do energy minimization after inflating the system i got the following result. Steepest Descents converged to machine precision in 15 steps, but did not reach the requested Fmax 1000. Potential Energy = 1.6157550e+17 Maximum force =inf on atom 2093 Norm of force =inf So the system is not converged well. I checked the output .gro file the protein came completely out of the bilayer. I tried to fix the problem by increasing the -fc value to 100 but still problem continues. Will you please tell me what will be the reason behind this problem and how to fix it. If the protein is completely out of the bilayer, that means you haven't built the system properly. EM will not cause massive displacement of any species, so a protein floating out in the middle of nowhere indicates it is incorrectly centered within the unit cell. -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] membrane simulation
On Thu, May 3, 2012 at 4:38 PM, scapr...@uniroma3.it wrote: Hi all, I'm new in Membrane simulations with Gromacs. I have to simulate a system made up of a protein just leant on a membrane patch which has previously been extended and made it free of periodicity (with trjconv). I'm reading the KALP15 in DPPCI Tutorial and, so far, I managed to obtain my protein (in pdb code) very close to the membrane surface by using editconf and cat command. At this point, I don't know how to get on. 1)How should I generate the topology file which includes the coordinates both of the protein and of the membrane? If you are using the ff53a6 FF then you need to add the appropriate lipid parameters in the ffnonbonded.itp and ffbonded.itp files (of ff53a6 FF) files which is very well explained in the tutorial. Then in your .top file you need to include the DPPC.itp. However, if you are using CHARMM36 FF, then you can directly use pdb2gmx on your system (I suppose DPPC is already included in it). If you wish to use the ff43a1 FF, then you can find the modified .itp files at https://sites.google.com/site/anirbanzz/gpcr-gromacs-tutorial . 2)Furthermore, the lipid molecules are listed in my pdb file with the abbreviation DPP, whereas I see that those ones are called DPPC in the Tutorial. Therefore, Should I replace DPP abbreviation with DPPC in my pdb file? Could this difference cause any bugs in the next steps? PDB files use three letter convention for residue names. I think you can change them without any issue in the .gro file. -Anirban Any suggestion would be appreciated, Silvia -- 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] membrane simulation
On 5/3/12 10:39 AM, scapr...@uniroma3.it wrote: Than you very much for your reply. I'm using ffnonbonded.itp etc. I still have some doubts regarding to the topology file which has to be used. Should I work and modify the topology file associated with the protein by adding the information related to the DPPC lipids as reported in the manual? I mean: is it ok if I use the topology file created at the beginning from pdb2gmx command on the protein and modify it? That is an appropriate workflow. The tutorial walks you through all the necessary steps, so do follow it carefully. -Justin -- 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
