[gmx-users] Channelrhodopsin topology
Hello everyone, I got some troubles with topology setup for channelrhodopsin setup in membrane. It is first such difficult system I met at my short scientific way and in fact it blocks my progress. I am not sure if gromacs mailing list is the way I should call for help, but perhaps I will find some answers here. Channelrhodopsin consists of protein, ligand (retinal) bounded to protein and there should be membrane. I want to make simulations in charmm ff. I found nice topology created by prof. Jochen Hub, but unfortunatly it is in amber ff. I have attached protein to membrane via charmm-gui, but I had to cut off the retinal (charmm gui couldn't handle ligand conected to protein). So I get nice structure and topology for both protein and membrane. Later I wanted to add retinal to the system - I made it manually, by coppying coordinates to gro file and getting topology to retinal from swiss-param. There are two problems - one is retinal and protein lives on their own. They do't see each other. On tail of retinal and tail of Lys296 (to which retinal is connected) there are too many hydrgens instead of bond. I just deleted it manually, but still I don't have parameters for this particular atoms. I don't know where to find them, how to get them. Also I have some mess in topology, beacuse some parts come from charmm-gui and retinal from swiss param. Any ideas how to make nice and managable topology files? And how should I connect retinal with lys296? With best regards, Wiktor -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] MD simulation of ligand only system
I want to make MD simulation on retinal molecule in all trans conformation. No protein, no water at all, just pure retinal. I found the structure in pubchem, downloaded 3d sdf, then created mol2 and put this molecule to swiss param server. I get bunch of files (pdb, itp etc.). I used editconf to generate gro from pdb. Now I want to use gromacs to make energy minimization. But when I try grompp I get Fatal error: Syntax error - File ret_all_trans.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes I thought that swiss-param will generate ready to go files. But it seems it's not. What should I do next? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] MD of ligand-only system
I want to make MD simulation on retinal molecule in all trans conformation. I found the structure in pubchem, downloaded 3d sdf, then created mol2 and put this molecule to swiss param server. I get bunch of files (pdb, itp etc.). Now I want to use gromacs to make simulation. But as far as I've seen simulation for only one ligand (Without protein, without water) should have diffrent commands. pdb2gmx doesn't work for example. Where to start with this? As I said - I've got pdb file and also itp file for charmm ff. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] grompp error: Unknown bond_atomtype
Cytowanie RAHUL SURESH : On Tue 26 Mar, 2019, 6:18 PM , wrote: Cytowanie RAHUL SURESH : > On Tue 26 Mar, 2019, 6:00 PM , wrote: > >> Hello everyone, >> >> I would call myself newbie gromacs user and need some help with task >> that was given to me. I'm supposed to take protein-ligand complex >> (bounded by covalence bond) and put it into membrane. I'm glad I've >> created the complex in amber force field. But now I stucked around >> membrane think. >> >> I have created DLPC-only membrane cluster in charmm-gui. I have found >> parameters for this type of lipid. I did add additional names for atom >> in atomtypes.atp, include ffbonded_lipid.itp and >> ffnonbonded_lipit.itp files to forcefrield.itp and put into amber >> forcefield directory t he lipids.rtp file. Gladly everything went >> smoothly with pdb2gmx with my membrane. I get topol.top file. Then I >> wanted to try minimize energy. I've prepared .mdp file and used gromp >> with: >> >> gmx grompp -f minim.mdp -c membrane_solv.gro -p topol.top -o em.tpr >> >> Unexpectedly I get error "Unknown bond_atomtype CTL3", though CTL3 is >> defined in atomtypes.atp and the bond have its parameters inside the >> ffbond.itp file. It's really strange for me, beacuse I thought that if >> topol.top file was created there is no possibility to get some >> troubles with defined atoms, bonds, etc. >> > This CTL3 is that of ligand? No, I'm doing right now ONLY membrane. There are only lipids in the .gro file with solvataion and the CTL3 is atom of lipid. I just wanted to check if I'm able to create membrane-only system first. If everything will work I'll try to embed protein+ligand in this membrane. If I believe you are using amber ff for the lipids generated using charm GUI, then I should say the nomenclature of the lipid membrane will be in charmm format. Either you must use charmm ff or you have to use lipids for amber ff .. I just download PDB file with membrane cluster structure from charmm-gui. No topology, no parameters at all. Only coordinates. Then I found parameters in amber force field for this DLPC and proceeded both pdb structure and parameters .itp with pdb2gmx. Everything worked. But now got troubles with energy minimization/simulations. >> > >> > > >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] grompp error: Unknown bond_atomtype
Cytowanie RAHUL SURESH : On Tue 26 Mar, 2019, 6:00 PM , wrote: Hello everyone, I would call myself newbie gromacs user and need some help with task that was given to me. I'm supposed to take protein-ligand complex (bounded by covalence bond) and put it into membrane. I'm glad I've created the complex in amber force field. But now I stucked around membrane think. I have created DLPC-only membrane cluster in charmm-gui. I have found parameters for this type of lipid. I did add additional names for atom in atomtypes.atp, include ffbonded_lipid.itp and ffnonbonded_lipit.itp files to forcefrield.itp and put into amber forcefield directory t he lipids.rtp file. Gladly everything went smoothly with pdb2gmx with my membrane. I get topol.top file. Then I wanted to try minimize energy. I've prepared .mdp file and used gromp with: gmx grompp -f minim.mdp -c membrane_solv.gro -p topol.top -o em.tpr Unexpectedly I get error "Unknown bond_atomtype CTL3", though CTL3 is defined in atomtypes.atp and the bond have its parameters inside the ffbond.itp file. It's really strange for me, beacuse I thought that if topol.top file was created there is no possibility to get some troubles with defined atoms, bonds, etc. This CTL3 is that of ligand? No, I'm doing right now ONLY membrane. There are only lipids in the .gro file with solvataion and the CTL3 is atom of lipid. I just wanted to check if I'm able to create membrane-only system first. If everything will work I'll try to embed protein+ligand in this membrane. Where did I make mistake? Have did you manage to add ligand topology? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] grompp error: Unknown bond_atomtype
Hello everyone, I would call myself newbie gromacs user and need some help with task that was given to me. I'm supposed to take protein-ligand complex (bounded by covalence bond) and put it into membrane. I'm glad I've created the complex in amber force field. But now I stucked around membrane think. I have created DLPC-only membrane cluster in charmm-gui. I have found parameters for this type of lipid. I did add additional names for atom in atomtypes.atp, include ffbonded_lipid.itp and ffnonbonded_lipit.itp files to forcefrield.itp and put into amber forcefield directory t he lipids.rtp file. Gladly everything went smoothly with pdb2gmx with my membrane. I get topol.top file. Then I wanted to try minimize energy. I've prepared .mdp file and used gromp with: gmx grompp -f minim.mdp -c membrane_solv.gro -p topol.top -o em.tpr Unexpectedly I get error "Unknown bond_atomtype CTL3", though CTL3 is defined in atomtypes.atp and the bond have its parameters inside the ffbond.itp file. It's really strange for me, beacuse I thought that if topol.top file was created there is no possibility to get some troubles with defined atoms, bonds, etc. Where did I make mistake? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
