[gmx-users] Using Amber Force Field in gromacs
Hi GROMACS users, I have generated topology and gromacs files using acpype.py .This is a membrane protein and thus to be simulated along with membrane. How can I use AMBER forcefield instead of GROMOS force field. Should I do the same as stated in the GROMACS tutorial in which GROMOS force field has been used? Please help me. Madhumita Das -- 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] extend simulation without tpbconv
Hi gmx-users, Is it possible to extend a simulation with change in the output control parameter (nstxtcout)? I am aware of that tpbconv can extend a simulation with the same output controls as in the input tpr file. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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] Using Amber Force Field in gromacs
madhumita das wrote: Hi GROMACS users, I have generated topology and gromacs files using acpype.py .This is a membrane protein and thus to be simulated along with membrane. How can I use AMBER forcefield instead of GROMOS force field. Should I do the same as stated in the GROMACS tutorial in which GROMOS force field has been used? You should not combine different force fields, so no, you should not simply follow that tutorial and attempt to use a ligand topology designed for an AMBER force field. The general workflow is largely the same, however, so you can apply the logic of the tutorial to whatever your system is. -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
Re: [gmx-users] Re: Preparation of the pure lipid system with charmm force field
James Starlight wrote: I've excluded charmm36.ff/lipids.rtp from my topology and obtain new error Fatal error: No such moleculetype POPC How I could include topology on this lipids ( all of them are present in the lipids.rtp. ) ? I have itp for the lipids only for the GROMOS ff so it should not be used here I presented the details of this procedure to you already: http://lists.gromacs.org/pipermail/gmx-users/2011-October/065311.html -Justin James 2011/10/21 Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au On 21/10/2011 5:41 PM, James Starlight wrote: I've also tried to make topology for my system parametriesed for charmm36 ff by hands but failed too :( This is my topology for the POPC bilayer wich I've made in VMD membrane builder as well as downloaded a pre built membrane system ( I've tested for both cases) ; Include chain topologies #include charmm36.ff/forcefield.itp ; Include lipids #include charmm36.ff/lipids.rtp .rtp files may not be #included ; Include water topology #include /charmm36.ff/tip3p.itp Initial backslash refers to the root of your file system, so is likely wrong. ; Include ion topologies #include charmm36.ff/ions.itp ; System specifications [ system ] 128-Lipid POPC Bilayer in water [ molecules ] POPC 72 When I've loaded my molecule to grompp I've obtained error Program grompp, VERSION 4.5.4 Source code file: /tmp/gromacs-4.5.4/src/kernel/__toppush.c, line: 770 Fatal error: Unknown bond_atomtype 1 What does it means? Is here anybody who also tried to parametriesed theis lipids by charmm ff ? Don't blame the ff yet :-) Mark -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists 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
Re: [gmx-users] Simulation of membrane protein
You'll learn far more by discovering it yourself. I stand by this statement. Perhaps some kind person with sufficient time on their hands will do your literature searching for you, but I do not, sorry. The information you need is out there. Start with the primary citation for whatever force field you want and search databases for citing articles or check out the references therein. Even Google can pull up very useful results within seconds, provided you've given sufficiently specific keywords. -Justin That's why at the present moment I'm examining different force fields and their implementation to the different systems. Could you recomend me some survey arcticle when I could find something usefull for this ? In particular I wounder to know about parametrisation for the membrane systems? Previosly I've found that charmm ff is ,ost accurasy in the case of such examination but I've not been able to rapametrise my bilayers via this ff yet ;x On other hand I have not difficulties with GROMOS ff for different systems ( e.g I've obtained very stabile systems durins some ns of simulations but I dont know about accuracy of the parametrisation of this ff in the case of membrane system for example . Finally I'm looking for tutorial for simulation of the pure lipids. E.g I want to simulate of different physical events on my membrane ( e.g I want to overkill my membrane by hyperpolarisation or other electrostatic effects emerged on the different steps of my simulation ) Could you also recomend me methodical literature for this styding? James -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists 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
Re: [gmx-users] Potential Energy Landscape
Natalie Stephenson wrote: Hi Justin (and gmx-users), I've been looking into using g_sham for the free energy landscapes, however I'm not sure what variables I should plot ... could I just use the g_energy (potential) outputs to produce the energy landscape?? Other examples I've seen using g_sham have done quite in depth eigenvector projections before plotting them using g_sham. The free energy of potential energy is probably not a meaningful quantity ;) What inputs would I require in order to determine how loading rate an increased loading rate on the simulation would change the force results? I know I'm probably being completely dumb but my use of maths has been sporadic to say the least in the last 7 years ... so getting back into it is proving more confusing! You haven't provided a lot of detail about what you're doing, what you've measured, or what you hope to achieve. In general, one plots two variables (one on each axis), and g_sham calculates a free energy based simply on the probability of occurrence of these values. For instance, for protein folding experiments, often the RMSD relative to the known structure is one variable, and something else like native contacts or hydrogen bonds is plotted as the other variable. The free energy surface is then generated as a function of intramolecular association and similarity to a known structure. -Justin Natalie Natalie Stephenson, B.Sc PhD Research Associate Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN x65816 From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 12 October 2011 18:22 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Potential Energy Landscape Natalie Stephenson wrote: I was recently told in passing that it would be possible to construct a 'potential energy landscape' from the simulations I have performed. This way I could remove any loading rate differences between simulations and experimental force experiments I've been performing ... however I cannot find anywhere in which this is mentioned. The only thing close I could find that was close was the free energy landscape using g_anaeig under the Dihedral PCA (http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca) however, I'm not sure this is what I'm looking for. Does anyone know where I would be able to find out / read more about how to create potential energy landscapes from my simulation outputs? g_sham produces free energy landscapes for any variables plotted against one another. -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 list gmx-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
Re: [gmx-users] Re: Preparation of the pure lipid system with charmm force field
Justin, In that way there was only one point wich was not understood for me In charmm I already have lipids.rtp with the parametries for my lipids. Also I have a single molecule of my lipid. How via pdb2gmx I could create parametrised itp file except of posre.itp ? James 2011/10/21 Justin A. Lemkul jalem...@vt.edu James Starlight wrote: I've excluded charmm36.ff/lipids.rtp from my topology and obtain new error Fatal error: No such moleculetype POPC How I could include topology on this lipids ( all of them are present in the lipids.rtp. ) ? I have itp for the lipids only for the GROMOS ff so it should not be used here I presented the details of this procedure to you already: http://lists.gromacs.org/**pipermail/gmx-users/2011-**October/065311.htmlhttp://lists.gromacs.org/pipermail/gmx-users/2011-October/065311.html -Justin James 2011/10/21 Mark Abraham mark.abra...@anu.edu.au mailto: mark.abra...@anu.edu.**au mark.abra...@anu.edu.au On 21/10/2011 5:41 PM, James Starlight wrote: I've also tried to make topology for my system parametriesed for charmm36 ff by hands but failed too :( This is my topology for the POPC bilayer wich I've made in VMD membrane builder as well as downloaded a pre built membrane system ( I've tested for both cases) ; Include chain topologies #include charmm36.ff/forcefield.itp ; Include lipids #include charmm36.ff/lipids.rtp .rtp files may not be #included ; Include water topology #include /charmm36.ff/tip3p.itp Initial backslash refers to the root of your file system, so is likely wrong. ; Include ion topologies #include charmm36.ff/ions.itp ; System specifications [ system ] 128-Lipid POPC Bilayer in water [ molecules ] POPC 72 When I've loaded my molecule to grompp I've obtained error Program grompp, VERSION 4.5.4 Source code file: /tmp/gromacs-4.5.4/src/kernel/**__toppush.c, line: 770 Fatal error: Unknown bond_atomtype 1 What does it means? Is here anybody who also tried to parametriesed theis lipids by charmm ff ? Don't blame the ff yet :-) Mark -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__**mailman/listinfo/gmx-usershttp://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__**Support/Mailing_Lists/Searchhttp://www.gromacs.org/__Support/Mailing_Lists/Search http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://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 mailto:gmx-users-request@**gromacs.orggmx-users-requ...@gromacs.org . Can't post? Read http://www.gromacs.org/__**Support/Mailing_Listshttp://www.gromacs.org/__Support/Mailing_Lists http://www.gromacs.org/**Support/Mailing_Listshttp://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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Re: Preparation of the pure lipid system with charmm force field
James Starlight wrote: Justin, In that way there was only one point wich was not understood for me In charmm I already have lipids.rtp with the parametries for my lipids. Also I have a single molecule of my lipid. How via pdb2gmx I could create parametrised itp file except of posre.itp ? If you don't need posre.itp, don't use it. What you really need is the topology for the lipid, which pdb2gmx will write for you, provided the input is syntactically correct and in agreement with the .rtp file. -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
Re: [gmx-users] Re: Preparation of the pure lipid system with charmm force field
So I should to use topol.top obtained for 1 lipid as the lipid.itp for the sustem contained of the same lipids, shouldnt I? 2011/10/21 Justin A. Lemkul jalem...@vt.edu James Starlight wrote: Justin, In that way there was only one point wich was not understood for me In charmm I already have lipids.rtp with the parametries for my lipids. Also I have a single molecule of my lipid. How via pdb2gmx I could create parametrised itp file except of posre.itp ? If you don't need posre.itp, don't use it. What you really need is the topology for the lipid, which pdb2gmx will write for you, provided the input is syntactically correct and in agreement with the .rtp file. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Re: Preparation of the pure lipid system with charmm force field
James Starlight wrote: So I should to use topol.top obtained for 1 lipid as the lipid.itp for the sustem contained of the same lipids, shouldnt I? A .top can be converted to a .itp which can then be included in a real system .top topology. So the lipid .top that you receive from pdb2gmx should be modified according to: http://www.gromacs.org/Documentation/File_Formats/.itp_File -Justin 2011/10/21 Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu James Starlight wrote: Justin, In that way there was only one point wich was not understood for me In charmm I already have lipids.rtp with the parametries for my lipids. Also I have a single molecule of my lipid. How via pdb2gmx I could create parametrised itp file except of posre.itp ? If you don't need posre.itp, don't use it. What you really need is the topology for the lipid, which pdb2gmx will write for you, provided the input is syntactically correct and in agreement with the .rtp file. -Justin -- ==__== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==__== -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org http://lists.gromacs.org/__mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/__Support/Mailing_Lists/Search 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 mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists 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
Re: [gmx-users] extend simulation without tpbconv
On 21/10/2011 10:49 PM, Chandan Choudhury wrote: Hi gmx-users, Is it possible to extend a simulation with change in the output control parameter (nstxtcout)? Yes, but not with tpbconv. Take your original .mdp file, change what you want, invoke grompp the same way. You can either give the checkpoint file to grompp -t or to mdrun -cpi depending what you are doing. Mark I am aware of that tpbconv can extend a simulation with the same output controls as in the input tpr file. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- 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] mismatch in coordinate and topology
Hi All, I am trying to minimize the chryptochrome structure that has one FAD and one MHF ligand bound to it. Following are the steps that I performed (1) Created the protein coordinate(gro) file using pdb2gmx command and choosing GROMOS43a1 force-field (2) Created the FAD and MHF topology and coordinate files using PRODRG where I have chosen a) no chirality, b) full charge and (c) no minimization. I have not seen any option for choosing force-field in the server. (3) I have taken the corresponding coordinate and topology files from that server, appended the coordinates of both the ligands in the gro file of the protein (before the box vector i.e. the last line), and also included the ligand topology files in the topol.top file after posre.itp and before spc.itpaccordingly. (4) I have also added two lines in the [molecules] section like, FAD 1 MHF 1 (5) Then I have created a cubic box where I have taken the coordinate and solvated the protein+ligands coordinate with spc water model using genbox. (6) Then I tried to create the em.tpr file from em.mdp file using grompp command. I got the following error message --- number of atoms in the coordinate file does not match with topology file where topology file has 31 missing atoms according to the numbers shown in the error message. I have checked the topology file after solvation and it is updated having the last line of the file with SOL 34741. I have been using gromacs for few months and I have successfully simulated systems with ligands before. Could anybody please tell me where I am doing wrong? thanks in advance Samrat -- 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] mismatch in coordinate and topology
Samrat Pal wrote: Hi All, I am trying to minimize the chryptochrome structure that has one FAD and one MHF ligand bound to it. Following are the steps that I performed (1) Created the protein coordinate(gro) file using pdb2gmx command and choosing GROMOS43a1 force-field (2) Created the FAD and MHF topology and coordinate files using PRODRG where I have chosen a) no chirality, b) full charge and (c) no minimization. /I have not seen any option for choosing force-field in the server/. (3) I have taken the corresponding coordinate and topology files from that server, appended the coordinates of both the ligands in the gro file of the protein (before the box vector i.e. the last line), and also included the ligand topology files in the topol.top file after posre.itp and before spc.itpaccordingly. Regarding (2) and (3) - the output of the PRODRG server will likely give poor results. See the paper linked from http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips. (4) I have also added two lines in the [molecules] section like, FAD 1 MHF 1 (5) Then I have created a cubic box where I have taken the coordinate and solvated the protein+ligands coordinate with spc water model using genbox. A dodecahedral box is likely going to be more efficient, but this is not relevant to the problem at hand. (6) Then I tried to create the em.tpr file from em.mdp file using grompp command. I got the following error message --- number of atoms in the coordinate file does not match with topology file where topology file has 31 missing atoms according to the numbers shown in the error message. OK, so do any of your molecules consist of 31 atoms? Do you get any notes about non-matching names? I have checked the topology file after solvation and it is updated having the last line of the file with SOL 34741. I have been using gromacs for few months and I have successfully simulated systems with ligands before. Could anybody please tell me where I am doing wrong? Did you properly increment the number of atoms in the coordinate file after adding your ligands? -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
Re: [gmx-users] Re: Preparation of the pure lipid system with charmm force field
Justin, So It seems that I've done all steps in accordance to that workflow and there have not been any more errors during loading my system in the gromp. :) By the way I have some methodological questions 1- Could you provide me with the source of the initial single lipids? Previously I've done my system based on the VMD plugin for bilayer constructing but I want to find single lipids and prepared my system by-hands. 2- Could you tell me other possible methods for self bi-layer preparation starting from initial single lipid molecule ? Thanks again, James -- 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] mismatch in coordinate and topology
Samrat Pal wrote: Hi Justin, (1) None of the ligands have 31 atoms - FAD has 86 atoms and MHF has 54 atoms. The error msg. does not show any specific mismatching. (2) I forgot to mention that I have increased the number of the atoms on the top (2nd line) of the gro file after adding the 2 ligands. Did you add any ions after solvation? And if so, did you update your topology? If SOL is the last entry, then likely not. -Justin Samrat *From:* Justin A. Lemkul jalem...@vt.edu *To:* Samrat Pal psamra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, October 21, 2011 8:49 AM *Subject:* Re: [gmx-users] mismatch in coordinate and topology Samrat Pal wrote: Hi All, I am trying to minimize the chryptochrome structure that has one FAD and one MHF ligand bound to it. Following are the steps that I performed (1) Created the protein coordinate(gro) file using pdb2gmx command and choosing GROMOS43a1 force-field (2) Created the FAD and MHF topology and coordinate files using PRODRG where I have chosen a) no chirality, b) full charge and (c) no minimization. /I have not seen any option for choosing force-field in the server/. (3) I have taken the corresponding coordinate and topology files from that server, appended the coordinates of both the ligands in the gro file of the protein (before the box vector i.e. the last line), and also included the ligand topology files in the topol.top file after posre.itp and before spc.itpaccordingly. Regarding (2) and (3) - the output of the PRODRG server will likely give poor results. See the paper linked from http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips. (4) I have also added two lines in the [molecules] section like, FAD 1 MHF 1 (5) Then I have created a cubic box where I have taken the coordinate and solvated the protein+ligands coordinate with spc water model using genbox. A dodecahedral box is likely going to be more efficient, but this is not relevant to the problem at hand. (6) Then I tried to create the em.tpr file from em.mdp file using grompp command. I got the following error message --- number of atoms in the coordinate file does not match with topology file where topology file has 31 missing atoms according to the numbers shown in the error message. OK, so do any of your molecules consist of 31 atoms? Do you get any notes about non-matching names? I have checked the topology file after solvation and it is updated having the last line of the file with SOL 34741. I have been using gromacs for few months and I have successfully simulated systems with ligands before. Could anybody please tell me where I am doing wrong? Did you properly increment the number of atoms in the coordinate file after adding your ligands? -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 -- 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] reg Hydrophobic interaction
vidhya sankar wrote: Dear Justin Thank you for your previous reply. As u mailed me already g_mindist of gromacs is the best tool to study about Hydrophobic contacts. From this i got only Average number of contacts. But i need the free energy of Hydrophobic interaction in energy units . I am doing umbrella pulling. Which Method is best to study Hydrophobic interaction energies That sounds like an application for an MM/PBSA type calculation. This is not something Gromacs can currently do, but you may be able to port your trajectory to other software that can. I have no experience doing this; maybe someone else can comment. -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
Re: [gmx-users] Re: Preparation of the pure lipid system with charmm force field
James Starlight wrote: Justin, So It seems that I've done all steps in accordance to that workflow and there have not been any more errors during loading my system in the gromp. :) By the way I have some methodological questions 1- Could you provide me with the source of the initial single lipids? Previously I've done my system based on the VMD plugin for bilayer constructing but I want to find single lipids and prepared my system by-hands. Here are several: http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources 2- Could you tell me other possible methods for self bi-layer preparation starting from initial single lipid molecule ? Packmol is a program that can build bilayers. You can also build crude monolayers with Gromacs that can be manipulated with genconf -nbox. These would require significant equilibration, as they are artificially crystalline. -Justin Thanks again, James -- 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] mismatch in coordinate and topology
Hi Justin, No. I have not added any ions. Samrat From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Friday, October 21, 2011 11:39 AM Subject: Re: [gmx-users] mismatch in coordinate and topology Samrat Pal wrote: Hi Justin, (1) None of the ligands have 31 atoms - FAD has 86 atoms and MHF has 54 atoms. The error msg. does not show any specific mismatching. (2) I forgot to mention that I have increased the number of the atoms on the top (2nd line) of the gro file after adding the 2 ligands. Did you add any ions after solvation? And if so, did you update your topology? If SOL is the last entry, then likely not. -Justin Samrat *From:* Justin A. Lemkul jalem...@vt.edu *To:* Samrat Pal psamra...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Friday, October 21, 2011 8:49 AM *Subject:* Re: [gmx-users] mismatch in coordinate and topology Samrat Pal wrote: Hi All, I am trying to minimize the chryptochrome structure that has one FAD and one MHF ligand bound to it. Following are the steps that I performed (1) Created the protein coordinate(gro) file using pdb2gmx command and choosing GROMOS43a1 force-field (2) Created the FAD and MHF topology and coordinate files using PRODRG where I have chosen a) no chirality, b) full charge and (c) no minimization. /I have not seen any option for choosing force-field in the server/. (3) I have taken the corresponding coordinate and topology files from that server, appended the coordinates of both the ligands in the gro file of the protein (before the box vector i.e. the last line), and also included the ligand topology files in the topol.top file after posre.itp and before spc.itpaccordingly. Regarding (2) and (3) - the output of the PRODRG server will likely give poor results. See the paper linked from http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips. (4) I have also added two lines in the [molecules] section like, FAD 1 MHF 1 (5) Then I have created a cubic box where I have taken the coordinate and solvated the protein+ligands coordinate with spc water model using genbox. A dodecahedral box is likely going to be more efficient, but this is not relevant to the problem at hand. (6) Then I tried to create the em.tpr file from em.mdp file using grompp command. I got the following error message --- number of atoms in the coordinate file does not match with topology file where topology file has 31 missing atoms according to the numbers shown in the error message. OK, so do any of your molecules consist of 31 atoms? Do you get any notes about non-matching names? I have checked the topology file after solvation and it is updated having the last line of the file with SOL 34741. I have been using gromacs for few months and I have successfully simulated systems with ligands before. Could anybody please tell me where I am doing wrong? Did you properly increment the number of atoms in the coordinate file after adding your ligands? -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 -- 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 list gmx-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 Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/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 list gmx-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
Re: [gmx-users] mismatch in coordinate and topology
Samrat Pal wrote: Hi Justin, No. I have not added any ions. Well, then it's a complete mystery. You'll have to go through your coordinate file and topology and count the relevant number of molecules or atoms and decide for yourself where the mismatch comes from. Nothing that you've provided explains where the problem comes from. -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
[gmx-users] POPC bilayer with Charmmff
Dear Gromacs users, I have downloaded the POPC bilayer molecular coordinates with charmmff equilibrated from Dr. Klauda's website. In this site it is mentioned Note: If you run these simulations in NAMD you MUST use NAMD 2.7b3 with vdw ForceSwitching turned on; what does vdw ForceSwitching turned on mean, is it related to adding few more parameters to mdp files? like rlist = 1.2 rlistlong = 1.4 rcoulomb= 1.2 rvdw= 1.0 vdwtype = switch rvdw_switch = 0.8 coulombtype = PME pme_order = 4 fourierspacing = 0.16 and , does this apply to gromacs also, if i use these lipid bilayers to run simulations in gromacs. I have one more question, i want to increase this bilayer containing 72 lipids to 250 lipids, so how can i do this or can i get it downloaded from any website like Dr.Klauda website Please let me know your suggestions. Thanks, Pramod -- 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] increase the time frame
Hi users, Iam running a minimization on protein complex in vacuum. i have set the parameters as following- ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steepest; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps= 5; Maximum number of (minimization) steps to perform nstenergy= 1 ; Write energies to disk every nstenergy steps energygrps= Protein; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstxout = 1 nstlist= 10; Frequency to update the neighbor list and long range forces ns_type= grid ; Method to determine neighbor list (simple, grid) rlist= 1.0; Cut-off for making neighbor list (short range forces) coulombtype= cutoff ; Treatment of long range electrostatic interactions rcoulomb= 1.0; long range electrostatic cut-off rvdw= 1.4; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= no; Periodic Boundary Conditions (yes/no) But from this i could write only 2 frames i need to increase the time frames, what is to be changed in the parameters. Thanks, Aiswarya -- 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] extending simulation with grompp incorporating velocities
On 21/10/2011 4:51 PM, Chandan Choudhury wrote: On Fri, Oct 21, 2011 at 10:26 AM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 21/10/2011 3:25 PM, Chandan Choudhury wrote: Dear gmx users, A simulation was performed for 50 ns with ; RUN CONTROL integrator = md nsteps = 5000 dt = 0.001 ; OUTPUT CONTROL nstxout = 1000 nstvout = 1000 nstxtcout= 0 nstlog = 100 nstenergy= 100 The output produced were 0-50.edr, 0-50.trr, 0-50.log, 0-50.pdb state.cpt, state_prev.cpt. The simulation completed normally. After 50 ns, I intend to extend for 4 more ns, write the trajectory file frequently with Use tpbconv -extend. See http://www.gromacs.org/Documentation/How-tos/Extending_Simulations I was aware with the tpbconv command. But while using the tpbconv command, we cannot change the output frequency. If somehow the trajectory writing frequency can be changed, it will solve my curiosity. Ah. Well for a new .mdp, you need the combination of nsteps, init_step and the step number in the .cpt to all make mutual sense, and perhaps tinit, etc. also. gmxdump -cp may help here. Note that tinit and init_step refer to the whole simulation, not the start of any non-initial chunk. Mark -- 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] Re: Preparation of the pure lipid system with charmm force field
I've also tried to make topology for my system parametriesed for charmm36 ff by hands but failed too :( This is my topology for the POPC bilayer wich I've made in VMD membrane builder as well as downloaded a pre built membrane system ( I've tested for both cases) ; Include chain topologies #include charmm36.ff/forcefield.itp ; Include lipids #include charmm36.ff/lipids.rtp ; Include water topology #include /charmm36.ff/tip3p.itp ; Include ion topologies #include charmm36.ff/ions.itp ; System specifications [ system ] 128-Lipid POPC Bilayer in water [ molecules ] POPC 72 When I've loaded my molecule to grompp I've obtained error Program grompp, VERSION 4.5.4 Source code file: /tmp/gromacs-4.5.4/src/kernel/toppush.c, line: 770 Fatal error: Unknown bond_atomtype 1 What does it means? Is here anybody who also tried to parametriesed theis lipids by charmm ff ? James 2011/10/20 James Starlight jmsstarli...@gmail.com Dear, Gromac's users! Today I've tried to make pure lipid bi-layer system from initial .pdb structure with the parametrization by the charmm ff. The main goal of this step is preparing the initial structure suitable for the futher simulation ( creating gro, top and posre files) First I've download s system consisted of 72 dppc lipids solved with water. Then I've succesfull created .gro as well as .top files by the pdb2grmx for my lipid system. But on futher during creatinon of the tpr file by gromp I've obtained many errors like this ERROR 4378 [file topol.top, line 83773]: No default U-B types Also I've tried to make my own bi-layer by VMD membrane plugin. After processing of this file by pdb2gmx I've obtained many .itp files like topol_Other_chain_L2.itp included in the generated topology file topol.top. But during loading this structure to the grompp I've obtained above mentioned error again. In both cases I've used mdp file for gromp consist of minimization algorithm ( attached). What I've done wrong? Could you provide me with the workable algorithm for preparation of the pure lipid system parametriezed by charm27 ? Finally I have small queation about charmm structures- I've found already pre-equilibrated bi-layers http://terpconnect.umd.edu/~jbklauda/research/download.html where each pdb file is accompanied by the PSF ones. As I've understood the PSF is the same to the top in the Gromacs. Could I convert PSF to the TOP for already pre-built system? Thanks for help James James -- 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] Re: Preparation of the pure lipid system with charmm force field
On 21/10/2011 5:41 PM, James Starlight wrote: I've also tried to make topology for my system parametriesed for charmm36 ff by hands but failed too :( This is my topology for the POPC bilayer wich I've made in VMD membrane builder as well as downloaded a pre built membrane system ( I've tested for both cases) ; Include chain topologies #include charmm36.ff/forcefield.itp ; Include lipids #include charmm36.ff/lipids.rtp .rtp files may not be #included ; Include water topology #include /charmm36.ff/tip3p.itp Initial backslash refers to the root of your file system, so is likely wrong. ; Include ion topologies #include charmm36.ff/ions.itp ; System specifications [ system ] 128-Lipid POPC Bilayer in water [ molecules ] POPC 72 When I've loaded my molecule to grompp I've obtained error Program grompp, VERSION 4.5.4 Source code file: /tmp/gromacs-4.5.4/src/kernel/toppush.c, line: 770 Fatal error: Unknown bond_atomtype 1 What does it means? Is here anybody who also tried to parametriesed theis lipids by charmm ff ? Don't blame the ff yet :-) Mark -- 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] increase the time frame
On 21/10/2011 5:09 PM, aiswarya pawar wrote: Hi users, Iam running a minimization on protein complex in vacuum. i have set the parameters as following- ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steepest; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps= 5; Maximum number of (minimization) steps to perform nstenergy= 1 ; Write energies to disk every nstenergy steps energygrps= Protein; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstxout = 1 nstlist= 10; Frequency to update the neighbor list and long range forces ns_type= grid ; Method to determine neighbor list (simple, grid) rlist= 1.0; Cut-off for making neighbor list (short range forces) coulombtype= cutoff ; Treatment of long range electrostatic interactions rcoulomb= 1.0; long range electrostatic cut-off rvdw= 1.4; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= no; Periodic Boundary Conditions (yes/no) But from this i could write only 2 frames i need to increase the time frames, what is to be changed in the parameters. This will write every frame of the EM, but if it only has two steps... Mark -- 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] increase the time frame
After running this minimization when i did gmxcheck i got this output trn version: GMX_trn_file (single precision) Reading frame 0 time9.000 # Atoms 4113 Reading frame 3 time 57.000 Timesteps at t=31 don't match (12, 26) Reading frame 4 time 69.000 Timesteps at t=57 don't match (26, 12) Reading frame 14 time 192.000 Timesteps at t=184 don't match (13, 8) Last frame 14 time 192.000 Item#frames Step15 Time15 Lambda 15 Coords 15 Velocities 0 Forces 0 Box 15 why is it saying that Timesteps at t=31 don't match (12, 26). On Fri, Oct 21, 2011 at 12:25 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 21/10/2011 5:09 PM, aiswarya pawar wrote: Hi users, Iam running a minimization on protein complex in vacuum. i have set the parameters as following- ; Lines starting with ';' ARE COMMENTS ; Everything following ';' is also comment title= Energy Minimization; Title of run ; The following line tell the program the standard locations where to find certain files cpp= /lib/cpp; Preprocessor ; Define can be used to control processes define = -DFLEXIBLE ; Parameters describing what to do, when to stop and what to save integrator= steepest; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1.0 kJ/mol emstep = 0.01 nsteps= 5; Maximum number of (minimization) steps to perform nstenergy= 1 ; Write energies to disk every nstenergy steps energygrps= Protein; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstxout = 1 nstlist= 10; Frequency to update the neighbor list and long range forces ns_type= grid ; Method to determine neighbor list (simple, grid) rlist= 1.0; Cut-off for making neighbor list (short range forces) coulombtype= cutoff ; Treatment of long range electrostatic interactions rcoulomb= 1.0; long range electrostatic cut-off rvdw= 1.4; long range Van der Waals cut-off constraints= none; Bond types to replace by constraints pbc= no; Periodic Boundary Conditions (yes/no) But from this i could write only 2 frames i need to increase the time frames, what is to be changed in the parameters. This will write every frame of the EM, but if it only has two steps... Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Simulation of membrane protein
Justin, thanks again for the information Different force fields require different settings, most notably cutoffs. Understanding the intrinsics of the chosen force field is a prerequisite for using it. Again, time spent in the literature here is more valuable than me spitting out settings that you should use. You'll learn far more by discovering it yourself. That's why at the present moment I'm examining different force fields and their implementation to the different systems. Could you recomend me some survey arcticle when I could find something usefull for this ? In particular I wounder to know about parametrisation for the membrane systems? Previosly I've found that charmm ff is ,ost accurasy in the case of such examination but I've not been able to rapametrise my bilayers via this ff yet ;x On other hand I have not difficulties with GROMOS ff for different systems ( e.g I've obtained very stabile systems durins some ns of simulations but I dont know about accuracy of the parametrisation of this ff in the case of membrane system for example . Finally I'm looking for tutorial for simulation of the pure lipids. E.g I want to simulate of different physical events on my membrane ( e.g I want to overkill my membrane by hyperpolarisation or other electrostatic effects emerged on the different steps of my simulation ) Could you also recomend me methodical literature for this styding? James -- ==**== 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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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
[gmx-users] Residue - ligand interaction energy
Dear Gmx Users, I run the simulation of my protein and ligands. I specified the energy groups of each of the residue of my protein. I would like to calculate the total interaction energy: V=V(electr)+V(vdw) for each residue and my ligands as a function of the distance between them. I am interested in the contribution of vdW and electrostatic interactions between them with respect to distance. Do you have any clue which command can deal with this? I thought about: 1. Using g_energy to calculate: SR-LJ and SR-electrostatic with respect to time 2. g_dist of COM of ligand and each residue with respect to time. Am I right or is there any direct tool which will calulate it? Thank you, Steven -- 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] Potential Energy Landscape
Hi Justin (and gmx-users), I've been looking into using g_sham for the free energy landscapes, however I'm not sure what variables I should plot ... could I just use the g_energy (potential) outputs to produce the energy landscape?? Other examples I've seen using g_sham have done quite in depth eigenvector projections before plotting them using g_sham. What inputs would I require in order to determine how loading rate an increased loading rate on the simulation would change the force results? I know I'm probably being completely dumb but my use of maths has been sporadic to say the least in the last 7 years ... so getting back into it is proving more confusing! Natalie Natalie Stephenson, B.Sc PhD Research Associate Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN x65816 From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: 12 October 2011 18:22 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Potential Energy Landscape Natalie Stephenson wrote: I was recently told in passing that it would be possible to construct a 'potential energy landscape' from the simulations I have performed. This way I could remove any loading rate differences between simulations and experimental force experiments I've been performing ... however I cannot find anywhere in which this is mentioned. The only thing close I could find that was close was the free energy landscape using g_anaeig under the Dihedral PCA (http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca) however, I'm not sure this is what I'm looking for. Does anyone know where I would be able to find out / read more about how to create potential energy landscapes from my simulation outputs? g_sham produces free energy landscapes for any variables plotted against one another. -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 -- 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] (no subject)
To whomsoever it may concern, I am trying to create the tip6p itp file. In order to do that, since it is an overlap of the tip4p and tip5p model (visually) I am trying to understand the a, b, and c values for the position of the dummy charge in the tip5p models. Below is the part of the script that is of my concern. _ [ dummies3 ] ; The position of the dummy is computed as follows: ; ; The distance from OW to L is 0.07 nm, the geometry is tetrahedral ; (109.47 deg) ; Therefore, a = b = 0.07 * cos (109.47/2) / | xOH1 + xOH2 | ; c = 0.07 * sin (109.47/2) / | xOH1 X xOH2 | ; =20 ; ; Using | xOH1 X xOH2 | = | xOH1 | | xOH2 | sin (H1-O-H2) ; | xOH1 + xOH2 | = 2 | xOH1 | cos (H1-O-H2) ; Dummy pos x4 = x1 + a*x21 + b*x31 + c*(x21 X x31) ; Dummy from funct a b c 4 1 2 3 4 -0.344908 -0.344908 -6.4437903493 5 1 2 3 4 -0.344908 -0.344908 6.4437903493 ___ I do understand everything except the bolded bit. so far i have understood that |xOH1| is the magnitude of OH on the x-axis, but putting those values in i don't the the correct a, b, c. I'm not good in vectors and i have had a look at the gromacs manual (the 3out model ni figure 4.16). I don't know where i am going wrong. I would appreciate the help thanks. Thanks, Pratik Kaku -- 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] TIP5P calculating the dummy positions
To whomsoever it may concern, I am trying to create the tip6p itp file. In order to do that, since it is an overlap of the tip4p and tip5p model (visually) I am trying to understand the a, b, and c values for the position of the dummy charge in the tip5p models. Below is the part of the script that is of my concern. _ [ dummies3 ] ; The position of the dummy is computed as follows: ; ; The distance from OW to L is 0.07 nm, the geometry is tetrahedral ; (109.47 deg) ; Therefore, a = b = 0.07 * cos (109.47/2) / | xOH1 + xOH2 | ; c = 0.07 * sin (109.47/2) / | xOH1 X xOH2 | ; =20 ; ; Using | xOH1 X xOH2 | = | xOH1 | | xOH2 | sin (H1-O-H2) ; | xOH1 + xOH2 | = 2 | xOH1 | cos (H1-O-H2) ; Dummy pos x4 = x1 + a*x21 + b*x31 + c*(x21 X x31) ; Dummy from funct a b c 4 1 2 3 4 -0.344908 -0.344908 -6.4437903493 5 1 2 3 4 -0.344908 -0.344908 6.4437903493 ___ I do understand everything except the bolded bit. so far i have understood that |xOH1| is the magnitude of OH on the x-axis, but putting those values in i don't the the correct a, b, c. I'm not good in vectors and i have had a look at the gromacs manual (the 3out model ni figure 4.16). I don't know where i am going wrong. I would appreciate the help thanks. Thanks, Pratik Kaku -- 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] TIP5P calculating the dummy positions
Dear Pratik, I am trying to create the tip6p itp file. In order to do that, since it is an overlap of the tip4p and tip5p model (visually) I am trying to understand the a, b, and c values for the position of the dummy charge in the tip5p models. Below is the part of the script that is of my concern. _ [ dummies3 ] ; The position of the dummy is computed as follows: ; ; The distance from OW to L is 0.07 nm, the geometry is tetrahedral ; (109.47 deg) ; Therefore, a = b = 0.07 * cos (109.47/2) / | xOH1 + xOH2 | xOH1 is the vector from O to H1, (not just the x component) | xOH1 + xOH2 | is normalisation factor as these vectors are not of unit length ; c = 0.07 * sin (109.47/2) / | xOH1 X xOH2 | again | xOH1 X xOH2 | is a normalisation factor as the cross product of the vector from O to H1 with the vector from O to H2 will not be a unit vector. ; =20 ; ; Using | xOH1 X xOH2 | = | xOH1 | | xOH2 | sin (H1-O-H2) This is a standard vector identity the modulus of the cross product of two vectors is the product of the moduli times the sine of the angle between them: |V X U| = |V||U|sin(theta) Hope that's helpful Richard ; | xOH1 + xOH2 | = 2 | xOH1 | cos (H1-O-H2) ; Dummy pos x4 = x1 + a*x21 + b*x31 + c*(x21 X x31) ; Dummy from funct a b c 4 1 2 3 4 -0.344908 -0.344908 -6.4437903493 5 1 2 3 4 -0.344908 -0.344908 6.4437903493 ___ I do understand everything except the bolded bit. so far i have understood that |xOH1| is the magnitude of OH on the x-axis, but putting those values in i don't the the correct a, b, c. I'm not good in vectors and i have had a look at the gromacs manual (the 3out model ni figure 4.16). I don't know where i am going wrong. I would appreciate the help thanks. Thanks, Pratik Kaku -- 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] Re: Preparation of the pure lipid system with charmm force field
I've excluded charmm36.ff/lipids.rtp from my topology and obtain new error Fatal error: No such moleculetype POPC How I could include topology on this lipids ( all of them are present in the lipids.rtp. ) ? I have itp for the lipids only for the GROMOS ff so it should not be used here James 2011/10/21 Mark Abraham mark.abra...@anu.edu.au On 21/10/2011 5:41 PM, James Starlight wrote: I've also tried to make topology for my system parametriesed for charmm36 ff by hands but failed too :( This is my topology for the POPC bilayer wich I've made in VMD membrane builder as well as downloaded a pre built membrane system ( I've tested for both cases) ; Include chain topologies #include charmm36.ff/forcefield.itp ; Include lipids #include charmm36.ff/lipids.rtp .rtp files may not be #included ; Include water topology #include /charmm36.ff/tip3p.itp Initial backslash refers to the root of your file system, so is likely wrong. ; Include ion topologies #include charmm36.ff/ions.itp ; System specifications [ system ] 128-Lipid POPC Bilayer in water [ molecules ] POPC 72 When I've loaded my molecule to grompp I've obtained error Program grompp, VERSION 4.5.4 Source code file: /tmp/gromacs-4.5.4/src/kernel/**toppush.c, line: 770 Fatal error: Unknown bond_atomtype 1 What does it means? Is here anybody who also tried to parametriesed theis lipids by charmm ff ? Don't blame the ff yet :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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
