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] 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] 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] 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
[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] 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
