Re: [gmx-users] g_wham error
Hi, Justin, Thanks for your answer. The problem is solved by dos2unix for the .dat files. Bests, Yuanyuan 发自我的 iPhone > 在 2017年2月19日，上午6:11，Justin Lemkul 写道： > > > >> On 2/18/17 4:22 AM, QU Yuanyuan wrote: >> Hi, >> >> >> I am doing umbrella sampling for my system and want to use g_wham to >> calculate pmf. After I finished the umbrella sampling, I obtained 9 tpr and >> 9 pullf files. As instructed, I constructed tpr-files.dat and >> pullf-files.dat containing these 9 tpr filenames and 9 pullf filenames. >> >> >> However, when I run "g_wham -if -it -o -hist -unit kT ",it does not run >> correctly, it terminates with error: >> >> >> "Source code file: >> /opt/software/gromacs-5.0.5/src/gromacs/gmxana/gmx_wham.cpp, line: 1767 >> >> Fatal error: .Should be tpr, xvg, or gdo." >> > > Given this fragmented error message, either you're retyping incompletely > (please just copy and paste) or it's a clue as to the problem. The code > should print out the offending file name. If this is actually what you're > getting, then your input in malformed in some way, but without seeing the > actual contents it's impossible to say. Make sure you're using normal > Unix-style line endings. > > -Justin > >> >> >> >> Then I checked the source code file of gmx_wham.cpp line:1767, which is the >> function to check the file type. >> >> >> I am confused as the filenames in the tpr-files.dat and pullf-files.dat I >> put are correct. >> >> >> Does anybody know what happened? Thanks very much! >> >> >> Bests, >> Yuanyuan >> >> -- >> Research Associate >> School of Physics, Shandong University >> >> >> >> >> >> >> > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] E. coli's Inner Membrane Lipid Selection
That seems like a sensible thing to do given what you are wanting to look at (and is what I would probably do too in your situation). I imagine what will be of far more importance than the membrane in your simulations, will be how you derive the parameters for the minocycline ligand and if they are good enough (although I can vaguely remember some decent looking CHARMM tetracycline parameters being published in the past, unless my memory completely deceives me). Good luck Tom On 19/02/17 00:33, Jonathan Saboury wrote: Thank you for so much great information! Coming from a organic synthesis background (knowing little to no biology) this gave me a lot of useful information. I'm looking to simulate 2DRD (AcrB cocomplexed with Minocycline) and study the interaction of the complex. Here is a picture of the complex: http://i66.tinypic.com/rwovwp.jpg (Minocycline is in the top half of the protein in CPK, the bilayer is the bottom half of the protein.) I think I'll start with 3:1 POPE:POPG, since the interaction I'm studying is pretty far away from the membrane, and the presence of the bilayer is probably just to stabilize the protein. If that fails I'll go to a more complex membrane. Thanks again for your time and help! - Jonathan On Sat, Feb 18, 2017 at 2:34 PM, Thomas Piggot wrote: Hi, For 1), perhaps but it depends upon what you are doing and what you are wanting to look at. Force field choice is (IMHO) likely to be more important (and CHARMM36 should be a good choice as long as you get all your mdp settings, etc., correct). For 2), the composition looks fairly reasonable bar a couple of points. I'm not aware of PS normally being a lipid found in E. coli, so I wouldn't have this. I'm not completely positive what the Y tail is in your/the CHARMM-GUI acronym (I think it is probably palmitoleoyl) but I believe cardiolipin should have a similar tail composition to PG, as in E. coli cardiolipin is synthesised directly from a combination of two PG's (unlike in mitochondria, where it is made de novo IIRC). So something more like PYPY for the four cardiolipin tails would likely give a better representation of the real system. To be honest, how complex you go with the membrane will likely depend upon what you want to do. A simple 75% POPE, 25% POPG is a fairly accurate representation of the membrane. I know there isn't a huge amount of oleoyl (18:1 delta9) tails in all the available E. coli experimental data, but oleoyl is a nice mix of the two most commonly found sn-2 chains: palmitoleoyl (16:1 delta 9) and cis-vaccenyl (18:1 delta 11). That said, if you want as accurate as possible, you can have all sorts of different types of lipid in there, with different tail types. At some stages in the cell cycle there are high amounts of cyclic rings in the tails instead of double-bonds, for example. Plus the ratio of PG:cardiolipin changes during the cell cycle too, as cardiolipin is synthesised and broken down (IIRC). Does, this matter? Would this impact upon your simulations (as per your question 1)? These really are questions for you to address. In my view, probably not a huge amount, but you can't really tell for sure in your case without extensive testing (e.g lots of different repeat simulations in each type of membrane, long enough to ensure convergence and a statistical comparison of the results you get for what you consider to be important properties that you want to compare). A lot of work, that probably isn't worth it. So, I guess my answer for both of these, is that it really depends upon what you are wanting to study. For 1), it is hard to tell without extensive testing for your example. For 2), how complex you go with your composition is also up to you and what you are wanting to look at. At the one extreme, a simple PC membrane could well be good enough, for example, if the protein has been shown to experimentally behave fine in this type of membrane. If you're not really sure, I would personally probably go with the simple 3:1 POPE:POPG mixture as a simple yet reasonable representation of the membrane. One step further up in terms of complexity would be to include cardiolipin and have some more realistic tails (1-palmitoyl 2-palmitoleoly and 1-palmitoyl 2-cis-vaccenyl plus perhaps some cyclic ringed tails in there too depending if there is a certain point in the cell-cycle you are wanting to study). Cheers Tom On 18/02/17 21:12, Jonathan Saboury wrote: Hello all, I'm trying to perform MD on a membrane protein AcrB. I am using charmm-gui to build the membrane but having difficulty deciding on membrane constituents. AcrB is a protein in E. coli's inner membrane: http://www.nature.com/nature/ journal/v419/n6907/images/nature01050-f5.2.jpg Based on the below literature, I have chosen the following membrane: PYPE 70%, PYPG 14%, DPPS 8%, TYCL2 8%. Characterization of the Escherichia coli membrane structure and function during fedbatch cultivation: https://www.ncbi.nlm.nih.gov/ pmc/art
Re: [gmx-users] Issues combining protein and membrane file?
On 2/18/17 7:34 PM, Sanim Rahman wrote: My apologies, I sent you the wrong file. Here is the right one. I made the edits and all the atoms are properly accounted for in VMD but they are not visible. Also when I used the inflategro script on it, only 148 atoms were read. Here is the command I used: perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat Here are the files I attached: Original- https://www.dropbox.com/s/aaj4q4efrjxmj3b/system.gro?dl=0 The number of atoms is wrong (note that VMD prints out an error message to this effect, you have 80188 atoms, not 80189) and your columns are misaligned starting with the lipids, so the content of the file is unintelligible. The .gro file format has a fixed format (see link posted previously) and all programs that read them expect that format. -Justin Inflated- https://www.dropbox.com/s/aiu89i1n5nj5bpp/system_inflated.gro?dl=0 Regards, Sanim Rahman On Sat, Feb 18, 2017 at 7:22 PM, Justin Lemkul wrote: On 2/18/17 6:55 PM, Sanim Rahman wrote: Thank you Justin, I was able to remove the velocities from my file but it still fails to read. I attached a dropbox link to my file if you have the time to take a look at it. https://www.dropbox.com/s/aaj4q4efrjxmj3b/system.gro?dl=0 The file needs a title line. The number of atoms must be the second line, not the first. http://manual.gromacs.org/documentation/2016.2/user-guide/fi le-formats.html#gro -Justin Thank you! Regards, Sanim Rahman On Sat, Feb 18, 2017 at 5:18 PM, Justin Lemkul wrote: On 2/18/17 4:46 PM, Sanim Rahman wrote: Hi all, I am trying to prepare a system for a MD simulation of an ion channel (Kv1.2) in a POPC lipid bilayer. I am struggling inserting the protein into the lipid membrane. I am currently trying the inflategro.pl approach done in the KALP15 tutorial. The first step with the prepared structural files was to combine them together using cat protein.gro lipid.gro > system.gro However, after combining them and loading them into VMD, my system has become distorted and only 151 atoms out 90131 atoms were read. Is there anything I can do to fix this issue? I believe it may have to do with the nomenclature of my script. The .gro file for my protein and lipid bilayer is not written in a consistent format: 421THR CA10936 4.791 7.926 7.910 421THR CB10937 4.822 7.797 7.831 421THROG110938 4.862 7.831 7.698 421THRHG110939 4.882 7.748 7.647 421THRCG210940 4.701 7.705 7.826 421THR C10941 4.754 7.892 8.055 421THR O110942 4.772 7.974 8.146 421THR O210943 4.649 7.808 8.074 1POPCC11 5.168 4.220 4.016 -0.2491 0.0715 0.4836 1POPCC22 4.942 4.276 3.936 0.1967 0.1087 -0.5850 1POPCC33 5.108 4.444 3.993 0.3211 0.0553 -0.2150 1POPCN44 5.085 4.311 3.935 0.2251 0.0126 -0.0777 1POPCC55 5.129 4.301 3.795 -0.0894 -0.4945 -0.1460 1POPCC66 5.280 4.304 3.767 0.0019 -0.2403 0.3568 1POPC OS77 5.354 4.422 3.799 0.0579 -0.0618 -0.4147 1POPCP88 5.512 4.403 3.778 0.1576 0.2198 0.0575 1POPC OM99 5.532 4.289 3.686 0.1757 -0.1049 0.4662 1POPC OM10 10 5.597 4.524 3.785 0.1671 0.2024 0.2449 1POPC OS11 11 5.526 4.331 3.921 0.4792 -0.0093 -0.0879 VMD is probably choking on the fact that some of your lines have velocity information (the lipids) and others (the protein) don't. Try stripping the velocities and appending just the coordinates. I updated the number of atoms in my system and removed nonessential lines as well. Also, would the inflategro procedure be appropriate for this simulation considering that I am inserting a +10,000 atom protein into a lipid membrane? Sure, we've done it with big systems, though the script is a bit of a memory hog, IIRC. Haven't used it in a while. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support /Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility I
Re: [gmx-users] Issues combining protein and membrane file?
My apologies, I sent you the wrong file. Here is the right one. I made the edits and all the atoms are properly accounted for in VMD but they are not visible. Also when I used the inflategro script on it, only 148 atoms were read. Here is the command I used: perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat Here are the files I attached: Original- https://www.dropbox.com/s/aaj4q4efrjxmj3b/system.gro?dl=0 Inflated- https://www.dropbox.com/s/aiu89i1n5nj5bpp/system_inflated.gro?dl=0 Regards, Sanim Rahman On Sat, Feb 18, 2017 at 7:22 PM, Justin Lemkul wrote: > > > On 2/18/17 6:55 PM, Sanim Rahman wrote: > >> Thank you Justin, >> >> I was able to remove the velocities from my file but it still fails to >> read. I attached a dropbox link to my file if you have the time to take a >> look at it. >> >> https://www.dropbox.com/s/aaj4q4efrjxmj3b/system.gro?dl=0 >> >> > The file needs a title line. The number of atoms must be the second line, > not the first. > > http://manual.gromacs.org/documentation/2016.2/user-guide/fi > le-formats.html#gro > > -Justin > > > Thank you! >> >> Regards, >> Sanim Rahman >> >> >> On Sat, Feb 18, 2017 at 5:18 PM, Justin Lemkul wrote: >> >> >>> >>> On 2/18/17 4:46 PM, Sanim Rahman wrote: >>> >>> Hi all, I am trying to prepare a system for a MD simulation of an ion channel (Kv1.2) in a POPC lipid bilayer. I am struggling inserting the protein into the lipid membrane. I am currently trying the inflategro.pl approach done in the KALP15 tutorial. The first step with the prepared structural files was to combine them together using cat protein.gro lipid.gro > system.gro However, after combining them and loading them into VMD, my system has become distorted and only 151 atoms out 90131 atoms were read. Is there anything I can do to fix this issue? I believe it may have to do with the nomenclature of my script. The .gro file for my protein and lipid bilayer is not written in a consistent format: 421THR CA10936 4.791 7.926 7.910 421THR CB10937 4.822 7.797 7.831 421THROG110938 4.862 7.831 7.698 421THRHG110939 4.882 7.748 7.647 421THRCG210940 4.701 7.705 7.826 421THR C10941 4.754 7.892 8.055 421THR O110942 4.772 7.974 8.146 421THR O210943 4.649 7.808 8.074 1POPCC11 5.168 4.220 4.016 -0.2491 0.0715 0.4836 1POPCC22 4.942 4.276 3.936 0.1967 0.1087 -0.5850 1POPCC33 5.108 4.444 3.993 0.3211 0.0553 -0.2150 1POPCN44 5.085 4.311 3.935 0.2251 0.0126 -0.0777 1POPCC55 5.129 4.301 3.795 -0.0894 -0.4945 -0.1460 1POPCC66 5.280 4.304 3.767 0.0019 -0.2403 0.3568 1POPC OS77 5.354 4.422 3.799 0.0579 -0.0618 -0.4147 1POPCP88 5.512 4.403 3.778 0.1576 0.2198 0.0575 1POPC OM99 5.532 4.289 3.686 0.1757 -0.1049 0.4662 1POPC OM10 10 5.597 4.524 3.785 0.1671 0.2024 0.2449 1POPC OS11 11 5.526 4.331 3.921 0.4792 -0.0093 -0.0879 VMD is probably choking on the fact that some of your lines have >>> velocity >>> information (the lipids) and others (the protein) don't. Try stripping >>> the >>> velocities and appending just the coordinates. >>> >>> I updated the number of atoms in my system and removed nonessential lines >>> as well. Also, would the inflategro procedure be appropriate for this simulation considering that I am inserting a +10,000 atom protein into a lipid membrane? Sure, we've done it with big systems, though the script is a bit of a >>> memory hog, IIRC. Haven't used it in a while. >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> == >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/Support >>> /Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sc
Re: [gmx-users] E. coli's Inner Membrane Lipid Selection
Thank you for so much great information! Coming from a organic synthesis background (knowing little to no biology) this gave me a lot of useful information. I'm looking to simulate 2DRD (AcrB cocomplexed with Minocycline) and study the interaction of the complex. Here is a picture of the complex: http://i66.tinypic.com/rwovwp.jpg (Minocycline is in the top half of the protein in CPK, the bilayer is the bottom half of the protein.) I think I'll start with 3:1 POPE:POPG, since the interaction I'm studying is pretty far away from the membrane, and the presence of the bilayer is probably just to stabilize the protein. If that fails I'll go to a more complex membrane. Thanks again for your time and help! - Jonathan On Sat, Feb 18, 2017 at 2:34 PM, Thomas Piggot wrote: > Hi, > > For 1), perhaps but it depends upon what you are doing and what you are > wanting to look at. Force field choice is (IMHO) likely to be more > important (and CHARMM36 should be a good choice as long as you get all your > mdp settings, etc., correct). > > For 2), the composition looks fairly reasonable bar a couple of points. > I'm not aware of PS normally being a lipid found in E. coli, so I wouldn't > have this. I'm not completely positive what the Y tail is in your/the > CHARMM-GUI acronym (I think it is probably palmitoleoyl) but I believe > cardiolipin should have a similar tail composition to PG, as in E. coli > cardiolipin is synthesised directly from a combination of two PG's (unlike > in mitochondria, where it is made de novo IIRC). So something more like > PYPY for the four cardiolipin tails would likely give a better > representation of the real system. To be honest, how complex you go with > the membrane will likely depend upon what you want to do. A simple 75% > POPE, 25% POPG is a fairly accurate representation of the membrane. I know > there isn't a huge amount of oleoyl (18:1 delta9) tails in all the > available E. coli experimental data, but oleoyl is a nice mix of the two > most commonly found sn-2 chains: palmitoleoyl (16:1 delta 9) and > cis-vaccenyl (18:1 delta 11). That said, if you want as accurate as > possible, you can have all sorts of different types of lipid in there, with > different tail types. At some stages in the cell cycle there are high > amounts of cyclic rings in the tails instead of double-bonds, for example. > Plus the ratio of PG:cardiolipin changes during the cell cycle too, as > cardiolipin is synthesised and broken down (IIRC). Does, this matter? Would > this impact upon your simulations (as per your question 1)? These really > are questions for you to address. In my view, probably not a huge amount, > but you can't really tell for sure in your case without extensive testing > (e.g lots of different repeat simulations in each type of membrane, long > enough to ensure convergence and a statistical comparison of the results > you get for what you consider to be important properties that you want to > compare). A lot of work, that probably isn't worth it. > > So, I guess my answer for both of these, is that it really depends upon > what you are wanting to study. For 1), it is hard to tell without extensive > testing for your example. For 2), how complex you go with your composition > is also up to you and what you are wanting to look at. At the one extreme, > a simple PC membrane could well be good enough, for example, if the protein > has been shown to experimentally behave fine in this type of membrane. If > you're not really sure, I would personally probably go with the simple 3:1 > POPE:POPG mixture as a simple yet reasonable representation of the > membrane. One step further up in terms of complexity would be to include > cardiolipin and have some more realistic tails (1-palmitoyl 2-palmitoleoly > and 1-palmitoyl 2-cis-vaccenyl plus perhaps some cyclic ringed tails in > there too depending if there is a certain point in the cell-cycle you are > wanting to study). > > Cheers > > Tom > > > On 18/02/17 21:12, Jonathan Saboury wrote: > >> Hello all, >> >> I'm trying to perform MD on a membrane protein AcrB. I am using charmm-gui >> to build the membrane but having difficulty deciding on membrane >> constituents. >> >> AcrB is a protein in E. coli's inner membrane: >> http://www.nature.com/nature/ >> journal/v419/n6907/images/nature01050-f5.2.jpg >> >> Based on the below literature, I have chosen the following membrane: PYPE >> 70%, PYPG 14%, DPPS 8%, TYCL2 8%. >> >> Characterization of the Escherichia coli membrane structure and function >> during fedbatch cultivation: https://www.ncbi.nlm.nih.gov/ >> pmc/articles/PMC514524/pdf/1475-2859-3-9.pdf >> >> My two main questions are: >> 1.) Does lipid choice affect MD simulation much? I'm using charmm36 >> 2.) Does my lipid selection make sense? If not, why and what would you >> use? >> >> Thank you for your time!! :-) >> > > -- > Dr Thomas Piggot > Visiting Fellow > University of Southampton, UK. > > -- > Gromacs Users mailing list > > * Please s
Re: [gmx-users] Issues combining protein and membrane file?
On 2/18/17 6:55 PM, Sanim Rahman wrote: Thank you Justin, I was able to remove the velocities from my file but it still fails to read. I attached a dropbox link to my file if you have the time to take a look at it. https://www.dropbox.com/s/aaj4q4efrjxmj3b/system.gro?dl=0 The file needs a title line. The number of atoms must be the second line, not the first. http://manual.gromacs.org/documentation/2016.2/user-guide/file-formats.html#gro -Justin Thank you! Regards, Sanim Rahman On Sat, Feb 18, 2017 at 5:18 PM, Justin Lemkul wrote: On 2/18/17 4:46 PM, Sanim Rahman wrote: Hi all, I am trying to prepare a system for a MD simulation of an ion channel (Kv1.2) in a POPC lipid bilayer. I am struggling inserting the protein into the lipid membrane. I am currently trying the inflategro.pl approach done in the KALP15 tutorial. The first step with the prepared structural files was to combine them together using cat protein.gro lipid.gro > system.gro However, after combining them and loading them into VMD, my system has become distorted and only 151 atoms out 90131 atoms were read. Is there anything I can do to fix this issue? I believe it may have to do with the nomenclature of my script. The .gro file for my protein and lipid bilayer is not written in a consistent format: 421THR CA10936 4.791 7.926 7.910 421THR CB10937 4.822 7.797 7.831 421THROG110938 4.862 7.831 7.698 421THRHG110939 4.882 7.748 7.647 421THRCG210940 4.701 7.705 7.826 421THR C10941 4.754 7.892 8.055 421THR O110942 4.772 7.974 8.146 421THR O210943 4.649 7.808 8.074 1POPCC11 5.168 4.220 4.016 -0.2491 0.0715 0.4836 1POPCC22 4.942 4.276 3.936 0.1967 0.1087 -0.5850 1POPCC33 5.108 4.444 3.993 0.3211 0.0553 -0.2150 1POPCN44 5.085 4.311 3.935 0.2251 0.0126 -0.0777 1POPCC55 5.129 4.301 3.795 -0.0894 -0.4945 -0.1460 1POPCC66 5.280 4.304 3.767 0.0019 -0.2403 0.3568 1POPC OS77 5.354 4.422 3.799 0.0579 -0.0618 -0.4147 1POPCP88 5.512 4.403 3.778 0.1576 0.2198 0.0575 1POPC OM99 5.532 4.289 3.686 0.1757 -0.1049 0.4662 1POPC OM10 10 5.597 4.524 3.785 0.1671 0.2024 0.2449 1POPC OS11 11 5.526 4.331 3.921 0.4792 -0.0093 -0.0879 VMD is probably choking on the fact that some of your lines have velocity information (the lipids) and others (the protein) don't. Try stripping the velocities and appending just the coordinates. I updated the number of atoms in my system and removed nonessential lines as well. Also, would the inflategro procedure be appropriate for this simulation considering that I am inserting a +10,000 atom protein into a lipid membrane? Sure, we've done it with big systems, though the script is a bit of a memory hog, IIRC. Haven't used it in a while. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support /Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Issues combining protein and membrane file?
Thank you Justin, I was able to remove the velocities from my file but it still fails to read. I attached a dropbox link to my file if you have the time to take a look at it. https://www.dropbox.com/s/aaj4q4efrjxmj3b/system.gro?dl=0 Thank you! Regards, Sanim Rahman On Sat, Feb 18, 2017 at 5:18 PM, Justin Lemkul wrote: > > > On 2/18/17 4:46 PM, Sanim Rahman wrote: > >> Hi all, >> >> I am trying to prepare a system for a MD simulation of an ion channel >> (Kv1.2) in a POPC lipid bilayer. I am struggling inserting the protein >> into >> the lipid membrane. I am currently trying the inflategro.pl approach done >> in the KALP15 tutorial. The first step with the prepared structural files >> was to combine them together using >> >> cat protein.gro lipid.gro > system.gro >> >> However, after combining them and loading them into VMD, my system has >> become distorted and only 151 atoms out 90131 atoms were read. Is there >> anything I can do to fix this issue? >> >> I believe it may have to do with the nomenclature of my script. The .gro >> file for my protein and lipid bilayer is not written in a consistent >> format: >> >> 421THR CA10936 4.791 7.926 7.910 >> 421THR CB10937 4.822 7.797 7.831 >> 421THROG110938 4.862 7.831 7.698 >> 421THRHG110939 4.882 7.748 7.647 >> 421THRCG210940 4.701 7.705 7.826 >> 421THR C10941 4.754 7.892 8.055 >> 421THR O110942 4.772 7.974 8.146 >> 421THR O210943 4.649 7.808 8.074 >> 1POPCC11 5.168 4.220 4.016 -0.2491 0.0715 0.4836 >> 1POPCC22 4.942 4.276 3.936 0.1967 0.1087 -0.5850 >> 1POPCC33 5.108 4.444 3.993 0.3211 0.0553 -0.2150 >> 1POPCN44 5.085 4.311 3.935 0.2251 0.0126 -0.0777 >> 1POPCC55 5.129 4.301 3.795 -0.0894 -0.4945 -0.1460 >> 1POPCC66 5.280 4.304 3.767 0.0019 -0.2403 0.3568 >> 1POPC OS77 5.354 4.422 3.799 0.0579 -0.0618 -0.4147 >> 1POPCP88 5.512 4.403 3.778 0.1576 0.2198 0.0575 >> 1POPC OM99 5.532 4.289 3.686 0.1757 -0.1049 0.4662 >> 1POPC OM10 10 5.597 4.524 3.785 0.1671 0.2024 0.2449 >> 1POPC OS11 11 5.526 4.331 3.921 0.4792 -0.0093 -0.0879 >> >> > VMD is probably choking on the fact that some of your lines have velocity > information (the lipids) and others (the protein) don't. Try stripping the > velocities and appending just the coordinates. > > I updated the number of atoms in my system and removed nonessential lines >> as well. Also, would the inflategro procedure be appropriate for this >> simulation considering that I am inserting a +10,000 atom protein into a >> lipid membrane? >> >> > Sure, we've done it with big systems, though the script is a bit of a > memory hog, IIRC. Haven't used it in a while. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] E. coli's Inner Membrane Lipid Selection
Hi, For 1), perhaps but it depends upon what you are doing and what you are wanting to look at. Force field choice is (IMHO) likely to be more important (and CHARMM36 should be a good choice as long as you get all your mdp settings, etc., correct). For 2), the composition looks fairly reasonable bar a couple of points. I'm not aware of PS normally being a lipid found in E. coli, so I wouldn't have this. I'm not completely positive what the Y tail is in your/the CHARMM-GUI acronym (I think it is probably palmitoleoyl) but I believe cardiolipin should have a similar tail composition to PG, as in E. coli cardiolipin is synthesised directly from a combination of two PG's (unlike in mitochondria, where it is made de novo IIRC). So something more like PYPY for the four cardiolipin tails would likely give a better representation of the real system. To be honest, how complex you go with the membrane will likely depend upon what you want to do. A simple 75% POPE, 25% POPG is a fairly accurate representation of the membrane. I know there isn't a huge amount of oleoyl (18:1 delta9) tails in all the available E. coli experimental data, but oleoyl is a nice mix of the two most commonly found sn-2 chains: palmitoleoyl (16:1 delta 9) and cis-vaccenyl (18:1 delta 11). That said, if you want as accurate as possible, you can have all sorts of different types of lipid in there, with different tail types. At some stages in the cell cycle there are high amounts of cyclic rings in the tails instead of double-bonds, for example. Plus the ratio of PG:cardiolipin changes during the cell cycle too, as cardiolipin is synthesised and broken down (IIRC). Does, this matter? Would this impact upon your simulations (as per your question 1)? These really are questions for you to address. In my view, probably not a huge amount, but you can't really tell for sure in your case without extensive testing (e.g lots of different repeat simulations in each type of membrane, long enough to ensure convergence and a statistical comparison of the results you get for what you consider to be important properties that you want to compare). A lot of work, that probably isn't worth it. So, I guess my answer for both of these, is that it really depends upon what you are wanting to study. For 1), it is hard to tell without extensive testing for your example. For 2), how complex you go with your composition is also up to you and what you are wanting to look at. At the one extreme, a simple PC membrane could well be good enough, for example, if the protein has been shown to experimentally behave fine in this type of membrane. If you're not really sure, I would personally probably go with the simple 3:1 POPE:POPG mixture as a simple yet reasonable representation of the membrane. One step further up in terms of complexity would be to include cardiolipin and have some more realistic tails (1-palmitoyl 2-palmitoleoly and 1-palmitoyl 2-cis-vaccenyl plus perhaps some cyclic ringed tails in there too depending if there is a certain point in the cell-cycle you are wanting to study). Cheers Tom On 18/02/17 21:12, Jonathan Saboury wrote: Hello all, I'm trying to perform MD on a membrane protein AcrB. I am using charmm-gui to build the membrane but having difficulty deciding on membrane constituents. AcrB is a protein in E. coli's inner membrane: http://www.nature.com/nature/ journal/v419/n6907/images/nature01050-f5.2.jpg Based on the below literature, I have chosen the following membrane: PYPE 70%, PYPG 14%, DPPS 8%, TYCL2 8%. Characterization of the Escherichia coli membrane structure and function during fedbatch cultivation: https://www.ncbi.nlm.nih.gov/ pmc/articles/PMC514524/pdf/1475-2859-3-9.pdf My two main questions are: 1.) Does lipid choice affect MD simulation much? I'm using charmm36 2.) Does my lipid selection make sense? If not, why and what would you use? Thank you for your time!! :-) -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Issues combining protein and membrane file?
On 2/18/17 4:46 PM, Sanim Rahman wrote: Hi all, I am trying to prepare a system for a MD simulation of an ion channel (Kv1.2) in a POPC lipid bilayer. I am struggling inserting the protein into the lipid membrane. I am currently trying the inflategro.pl approach done in the KALP15 tutorial. The first step with the prepared structural files was to combine them together using cat protein.gro lipid.gro > system.gro However, after combining them and loading them into VMD, my system has become distorted and only 151 atoms out 90131 atoms were read. Is there anything I can do to fix this issue? I believe it may have to do with the nomenclature of my script. The .gro file for my protein and lipid bilayer is not written in a consistent format: 421THR CA10936 4.791 7.926 7.910 421THR CB10937 4.822 7.797 7.831 421THROG110938 4.862 7.831 7.698 421THRHG110939 4.882 7.748 7.647 421THRCG210940 4.701 7.705 7.826 421THR C10941 4.754 7.892 8.055 421THR O110942 4.772 7.974 8.146 421THR O210943 4.649 7.808 8.074 1POPCC11 5.168 4.220 4.016 -0.2491 0.0715 0.4836 1POPCC22 4.942 4.276 3.936 0.1967 0.1087 -0.5850 1POPCC33 5.108 4.444 3.993 0.3211 0.0553 -0.2150 1POPCN44 5.085 4.311 3.935 0.2251 0.0126 -0.0777 1POPCC55 5.129 4.301 3.795 -0.0894 -0.4945 -0.1460 1POPCC66 5.280 4.304 3.767 0.0019 -0.2403 0.3568 1POPC OS77 5.354 4.422 3.799 0.0579 -0.0618 -0.4147 1POPCP88 5.512 4.403 3.778 0.1576 0.2198 0.0575 1POPC OM99 5.532 4.289 3.686 0.1757 -0.1049 0.4662 1POPC OM10 10 5.597 4.524 3.785 0.1671 0.2024 0.2449 1POPC OS11 11 5.526 4.331 3.921 0.4792 -0.0093 -0.0879 VMD is probably choking on the fact that some of your lines have velocity information (the lipids) and others (the protein) don't. Try stripping the velocities and appending just the coordinates. I updated the number of atoms in my system and removed nonessential lines as well. Also, would the inflategro procedure be appropriate for this simulation considering that I am inserting a +10,000 atom protein into a lipid membrane? Sure, we've done it with big systems, though the script is a bit of a memory hog, IIRC. Haven't used it in a while. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Question regarding coarse-graining and all-atom structure
On 2/18/17 2:39 PM, ali.khourshae...@student.sharif.edu wrote: Dear Gromacs users, Is there any script I can use to coarse-grain ( based on martini forcefield) my lipid bilayer all-atom structure ( based on berger force field)? I know Martinize.py has been published, But it is confined to Protein I think. Maybe http://www.cgmartini.nl/index.php/downloads/tools/239-insane is what you want. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Question regarding the minimization of the system
On 2/18/17 2:42 PM, ali.khourshae...@student.sharif.edu wrote: Dear Gromacs users, During surfing the Internet, I found a Draft of an paper. Within it, for minimization of lipid bilayer system, they first remove the periodicity by the use of trjconv and then use mdrun to minimize it. I think it's false. But, I just want to make sure of it. mdrun doesn't care if molecules are whole or not. The .tpr has topology information, so connectivity is known and the physics is carried out correctly regardless of our visualization convenience. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Doubt from topology creation using g_x2top
On 2/18/17 1:26 PM, rakesh.p...@students.iiserpune.ac.in wrote: Dear all, I am trying to create a topology for a molecule using g_x2top and have defined all the atoms with connectivity in atomname.n2t file with different opls no. for all different types of atoms. But when I create topology, it does not identify all different atomtypes and takes one common opls no. for some of the atoms. This means your .n2t file does not correctly (or uniquely) specify the atom connectivity in a way that g_x2top can resolve correctly. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] residuetypes.dat file problem
On 2/18/17 12:41 PM, Mishelle Oña wrote: Hello everyone, I am modifying a force field to simulate a Polymer. I have add the monomers of my polymer in residuetypes.dat file as follows: ETHB Polymer ETHP Polymer ETHE Polymer When I run the pdb2gro command a message like this appears: Processing chain 1 (153 atoms, 30 residues) Warning: Starting residue PLAB1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue PLAP2 in chain not identified as Protein/RNA/DNA. Warning: Starting residue PLAP3 in chain not identified as Protein/RNA/DNA. Warning: Starting residue PLAP4 in chain not identified as Protein/RNA/DNA. Warning: Starting residue PLAP5 in chain not identified as Protein/RNA/DNA. More than 5 unidentified residues at start of chain - disabling further warnings Please could you help me with this problem? There isn't a problem. pdb2gmx is being a little too noisy in this instance, but it is true that "Polymer" is neither Protein, DNA, nor RNA. You don't necessarily have to do anything in residuetypes.dat for a polymer system. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_wham error
On 2/18/17 4:22 AM, QU Yuanyuan wrote: Hi, I am doing umbrella sampling for my system and want to use g_wham to calculate pmf. After I finished the umbrella sampling, I obtained 9 tpr and 9 pullf files. As instructed, I constructed tpr-files.dat and pullf-files.dat containing these 9 tpr filenames and 9 pullf filenames. However, when I run "g_wham -if -it -o -hist -unit kT ",it does not run correctly, it terminates with error: "Source code file: /opt/software/gromacs-5.0.5/src/gromacs/gmxana/gmx_wham.cpp, line: 1767 Fatal error: .Should be tpr, xvg, or gdo." Given this fragmented error message, either you're retyping incompletely (please just copy and paste) or it's a clue as to the problem. The code should print out the offending file name. If this is actually what you're getting, then your input in malformed in some way, but without seeing the actual contents it's impossible to say. Make sure you're using normal Unix-style line endings. -Justin Then I checked the source code file of gmx_wham.cpp line:1767, which is the function to check the file type. I am confused as the filenames in the tpr-files.dat and pullf-files.dat I put are correct. Does anybody know what happened? Thanks very much! Bests, Yuanyuan -- Research Associate School of Physics, Shandong University -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] PROTEIN-LIGAND SIMULATION
On 2/17/17 8:43 AM, Subashini .K wrote: Hi gromacs users, In order to calculate binding energy of single protein inhibitor complex through simulations, how long should we run the calculations? Is 2ns sufficient? The answer to this question is always: "have the observables of interest converged?" How to obtain results and plot time (in ps) along x-axis and binding energy (kJ/mol)along y-axis? If you're looking for a binding free energy, you can try an MM/PBSA post-processing calculation, but the standard for doing this is a series of free energy calculations (either alchemical perturbation or a PMF). A single, 2-ns MD run of a protein-ligand complex is unlikely to yield any sort of reliable result. I doubt the system is even fully relaxed over such a short time period. -Justin Had completed two equilibration phases (NVT and NPT)and then used the command for production MD (for 2ns). Can someone help? Thanks, Subashini.K -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Issues combining protein and membrane file?
Hi all, I am trying to prepare a system for a MD simulation of an ion channel (Kv1.2) in a POPC lipid bilayer. I am struggling inserting the protein into the lipid membrane. I am currently trying the inflategro.pl approach done in the KALP15 tutorial. The first step with the prepared structural files was to combine them together using cat protein.gro lipid.gro > system.gro However, after combining them and loading them into VMD, my system has become distorted and only 151 atoms out 90131 atoms were read. Is there anything I can do to fix this issue? I believe it may have to do with the nomenclature of my script. The .gro file for my protein and lipid bilayer is not written in a consistent format: 421THR CA10936 4.791 7.926 7.910 421THR CB10937 4.822 7.797 7.831 421THROG110938 4.862 7.831 7.698 421THRHG110939 4.882 7.748 7.647 421THRCG210940 4.701 7.705 7.826 421THR C10941 4.754 7.892 8.055 421THR O110942 4.772 7.974 8.146 421THR O210943 4.649 7.808 8.074 1POPCC11 5.168 4.220 4.016 -0.2491 0.0715 0.4836 1POPCC22 4.942 4.276 3.936 0.1967 0.1087 -0.5850 1POPCC33 5.108 4.444 3.993 0.3211 0.0553 -0.2150 1POPCN44 5.085 4.311 3.935 0.2251 0.0126 -0.0777 1POPCC55 5.129 4.301 3.795 -0.0894 -0.4945 -0.1460 1POPCC66 5.280 4.304 3.767 0.0019 -0.2403 0.3568 1POPC OS77 5.354 4.422 3.799 0.0579 -0.0618 -0.4147 1POPCP88 5.512 4.403 3.778 0.1576 0.2198 0.0575 1POPC OM99 5.532 4.289 3.686 0.1757 -0.1049 0.4662 1POPC OM10 10 5.597 4.524 3.785 0.1671 0.2024 0.2449 1POPC OS11 11 5.526 4.331 3.921 0.4792 -0.0093 -0.0879 I updated the number of atoms in my system and removed nonessential lines as well. Also, would the inflategro procedure be appropriate for this simulation considering that I am inserting a +10,000 atom protein into a lipid membrane? Regards, *Sanim Rahman* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] E. coli's Inner Membrane Lipid Selection
Hello all, I'm trying to perform MD on a membrane protein AcrB. I am using charmm-gui to build the membrane but having difficulty deciding on membrane constituents. AcrB is a protein in E. coli's inner membrane: http://www.nature.com/nature/ journal/v419/n6907/images/nature01050-f5.2.jpg Based on the below literature, I have chosen the following membrane: PYPE 70%, PYPG 14%, DPPS 8%, TYCL2 8%. Characterization of the Escherichia coli membrane structure and function during fedbatch cultivation: https://www.ncbi.nlm.nih.gov/ pmc/articles/PMC514524/pdf/1475-2859-3-9.pdf My two main questions are: 1.) Does lipid choice affect MD simulation much? I'm using charmm36 2.) Does my lipid selection make sense? If not, why and what would you use? Thank you for your time!! :-) -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Question regarding the minimization of the system
Dear Gromacs users, During surfing the Internet, I found a Draft of an paper. Within it, for minimization of lipid bilayer system, they first remove the periodicity by the use of trjconv and then use mdrun to minimize it. I think it's false. But, I just want to make sure of it. Sincerely, Ali -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Question regarding coarse-graining and all-atom structure
Dear Gromacs users, Is there any script I can use to coarse-grain ( based on martini forcefield) my lipid bilayer all-atom structure ( based on berger force field)? I know Martinize.py has been published, But it is confined to Protein I think. Sincerely, Ali -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Doubt from topology creation using g_x2top
Dear all, I am trying to create a topology for a molecule using g_x2top and have defined all the atoms with connectivity in atomname.n2t file with different opls no. for all different types of atoms. But when I create topology, it does not identify all different atomtypes and takes one common opls no. for some of the atoms. Thanks Rakesh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] residuetypes.dat file problem
Hello everyone, I am modifying a force field to simulate a Polymer. I have add the monomers of my polymer in residuetypes.dat file as follows: ETHB Polymer ETHP Polymer ETHE Polymer When I run the pdb2gro command a message like this appears: Processing chain 1 (153 atoms, 30 residues) Warning: Starting residue PLAB1 in chain not identified as Protein/RNA/DNA. Warning: Starting residue PLAP2 in chain not identified as Protein/RNA/DNA. Warning: Starting residue PLAP3 in chain not identified as Protein/RNA/DNA. Warning: Starting residue PLAP4 in chain not identified as Protein/RNA/DNA. Warning: Starting residue PLAP5 in chain not identified as Protein/RNA/DNA. More than 5 unidentified residues at start of chain - disabling further warnings Please could you help me with this problem? Thanks! Mishelle -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_wham error
Hi, I am doing umbrella sampling for my system and want to use g_wham to calculate pmf. After I finished the umbrella sampling, I obtained 9 tpr and 9 pullf files. As instructed, I constructed tpr-files.dat and pullf-files.dat containing these 9 tpr filenames and 9 pullf filenames. However, when I run "g_wham -if -it -o -hist -unit kT ",it does not run correctly, it terminates with error: "Source code file: /opt/software/gromacs-5.0.5/src/gromacs/gmxana/gmx_wham.cpp, line: 1767 Fatal error: .Should be tpr, xvg, or gdo." Then I checked the source code file of gmx_wham.cpp line:1767, which is the function to check the file type. I am confused as the filenames in the tpr-files.dat and pullf-files.dat I put are correct. Does anybody know what happened? Thanks very much! Bests, Yuanyuan -- Research Associate School of Physics, Shandong University -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
