[gmx-users] CHARMM-GUI to GROMACS
Dear all, I built up my protein in lipid bilayer by CHARMM-GUI and now I want to do equilibration by GROMACS. I know GROMACS can build the system, but my subsequent production run must be conducted by CHARMM. I want to use GROMACS to do equilibration cuz it may take long to get it equilibrated. Now I get stuck in some problems. 1) I'm not quite sure about how to make conversion. I searched the archive of the forum. Someone recommended I split the pdb generated by CHARMM-GUI into different pdb files for protein, lipid, water and ions, and use pdb2gmx to convert them to gro files individually. Then combine those gro files and made *.top file manually. Someone also suggested I convert original pdb directly to gro. Which one is better? 2) I tried both protocols. When I checked the robustness of my structure by grompp, problems came. As CHARMM-GUI uses TIP3P and it would be better to use TIPS3P with lipid (we have tested them with CHARMM36 force field), I'm not sure how to change water model. Another problem, the most troublesome, is that all water molecules whose residue ID's after could not be properly designated (say waters 1TIP to 10009TIP become 1000TIP which has 30 atoms). I don't know why it happened. Is there anything wrong with my converting logic in question 1)? I mean, I should not convert water or ions, should I? 3) CHARMM-GUI uses rectangular or hexagonal boxes but they are supported by GROMACS. I'm wondering whether there is any direct way to match the box type in GROMACS. Any comment or suggestion will be appreciated. Thanks. Best -- *Zhi Yue* Graduate Research Assistant Computer-Aided Drug Design Center School of Pharmacy University of Maryland 20 Penn St, Rm S612 Baltimore, MD 21201 Email:zhi...@umaryland.edu, zhi...@umd.edu -- 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] CHARMM-GUI to GROMACS
On 10/21/13 11:14 AM, Zhi Yue wrote: Dear all, I built up my protein in lipid bilayer by CHARMM-GUI and now I want to do equilibration by GROMACS. I know GROMACS can build the system, but my subsequent production run must be conducted by CHARMM. I want to use GROMACS to do equilibration cuz it may take long to get it equilibrated. Now I get stuck in some problems. 1) I'm not quite sure about how to make conversion. I searched the archive of the forum. Someone recommended I split the pdb generated by CHARMM-GUI into different pdb files for protein, lipid, water and ions, and use pdb2gmx to convert them to gro files individually. Then combine those gro files and made *.top file manually. Someone also suggested I convert original pdb directly to gro. Which one is better? Whichever one makes sense to you. I prefer a clean approach where you deal with one molecule at a time, but others do it differently. There's really no need to have pdb2gmx run through all the water, ions, etc. when really their topologies can easily be handled with simple #include statements. 2) I tried both protocols. When I checked the robustness of my structure by grompp, problems came. As CHARMM-GUI uses TIP3P and it would be better to use TIPS3P with lipid (we have tested them with CHARMM36 force field), I'm not sure how to change water model. Another problem, the most troublesome, You change the water model by #including the right topology, hence my approach above. The CHARMM27 distribution that is built into Gromacs uses tip3p.itp for the classic model and tips3p.itp for the CHARMM-specific model. Our lab recently released a full CHARMM36 force field, with tip3p.itp containing both models, toggled by using #ifdef blocks. is that all water molecules whose residue ID's after could not be properly designated (say waters 1TIP to 10009TIP become 1000TIP which has 30 atoms). I don't know why it happened. Is there anything wrong with my converting logic in question 1)? I mean, I should not convert water or ions, should I? The residue numbering is irrelevant, and is simply an outcome of PDB format, which only allows for 5 digits in residue numbers. It has no implications for the soundness of the topology or the simulation. 3) CHARMM-GUI uses rectangular or hexagonal boxes but they are supported by GROMACS. I'm wondering whether there is any direct way to match the box type in GROMACS. Both are supported natively. See manual section 3.2 and figure 3.2. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] CHARMM-GUI to GROMACS
Hi Justin, Thanks for your advice. I'll try again. Have a wonderful night! Best Shane On Mon, Oct 21, 2013 at 6:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/21/13 11:14 AM, Zhi Yue wrote: Dear all, I built up my protein in lipid bilayer by CHARMM-GUI and now I want to do equilibration by GROMACS. I know GROMACS can build the system, but my subsequent production run must be conducted by CHARMM. I want to use GROMACS to do equilibration cuz it may take long to get it equilibrated. Now I get stuck in some problems. 1) I'm not quite sure about how to make conversion. I searched the archive of the forum. Someone recommended I split the pdb generated by CHARMM-GUI into different pdb files for protein, lipid, water and ions, and use pdb2gmx to convert them to gro files individually. Then combine those gro files and made *.top file manually. Someone also suggested I convert original pdb directly to gro. Which one is better? Whichever one makes sense to you. I prefer a clean approach where you deal with one molecule at a time, but others do it differently. There's really no need to have pdb2gmx run through all the water, ions, etc. when really their topologies can easily be handled with simple #include statements. 2) I tried both protocols. When I checked the robustness of my structure by grompp, problems came. As CHARMM-GUI uses TIP3P and it would be better to use TIPS3P with lipid (we have tested them with CHARMM36 force field), I'm not sure how to change water model. Another problem, the most troublesome, You change the water model by #including the right topology, hence my approach above. The CHARMM27 distribution that is built into Gromacs uses tip3p.itp for the classic model and tips3p.itp for the CHARMM-specific model. Our lab recently released a full CHARMM36 force field, with tip3p.itp containing both models, toggled by using #ifdef blocks. is that all water molecules whose residue ID's after could not be properly designated (say waters 1TIP to 10009TIP become 1000TIP which has 30 atoms). I don't know why it happened. Is there anything wrong with my converting logic in question 1)? I mean, I should not convert water or ions, should I? The residue numbering is irrelevant, and is simply an outcome of PDB format, which only allows for 5 digits in residue numbers. It has no implications for the soundness of the topology or the simulation. 3) CHARMM-GUI uses rectangular or hexagonal boxes but they are supported by GROMACS. I'm wondering whether there is any direct way to match the box type in GROMACS. Both are supported natively. See manual section 3.2 and figure 3.2. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- 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 -- *Zhi Yue* Graduate Research Assistant Computer-Aided Drug Design Center School of Pharmacy University of Maryland 20 Penn St, Rm S612 Baltimore, MD 21201 Email:zhi...@umaryland.edu, zhi...@umd.edu -- 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] charmm-gui and gromacs
Dear: If I have used the charmm-gui to build the bilayer for the receptor-ligand complex,can I load the outcome to the gromacs to perform MD?Is the process complicated? How do it? Thanks! -- 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] charmm-gui and gromacs
On 13/02/2012 12:15 PM, xiaojiong wrote: Dear: If I have used the charmm-gui to build the bilayer for the receptor-ligand complex,can I load the outcome to the gromacs to perform MD?Is the process complicated? How do it? Thanks! You can probably write a .pdb coordinate file from any tool and read it with any GROMACS tool. Constructing your topology will be harder, and for grompp you will need the atom and residue naming to match that of your coordinate file. 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] CHARMM GUI to Gromacs
Dear all, I would like to simulate my protein in a lipid bilayer using gromacs 4.5.4, and a forcefield of gromos96. However i don't have the topologies files for lipid bilayer for POPE and DMPE. Anybody knows where can i get the topologies file for POPE and DMPE ? Before that, i had actually used the CHARMM GUI to put my protein into the lipid bilayer. From there, i am not sure how i am able to use the output from CHARMM GUI to do md simulation in gromacs Any help is much appreciated. Thanks a lot! -- 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] CHARMM GUI to Gromacs
There is already tutorial for creating lipid bilayer and insertion of protein into that for GROMACS http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html Why you have used Charmmgui I am not able to understand. You can get some useful topologies from below link,but I don't know how useful it might be for your case. http://people.ucalgary.ca/~tieleman/download.html On Mon, Oct 17, 2011 at 14:31, Roy Lee royle...@gmail.com wrote: Dear all, I would like to simulate my protein in a lipid bilayer using gromacs 4.5.4, and a forcefield of gromos96. However i don't have the topologies files for lipid bilayer for POPE and DMPE. Anybody knows where can i get the topologies file for POPE and DMPE ? Before that, i had actually used the CHARMM GUI to put my protein into the lipid bilayer. From there, i am not sure how i am able to use the output from CHARMM GUI to do md simulation in gromacs Any help is much appreciated. Thanks a lot! -- 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 -- --- Regards, Bipin Singh -- 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
