Re: [gmx-users] grompp error: Unknown bond_atomtype
On 4/1/19 5:28 AM, vico...@fizyka.umk.pl wrote: Dear Professor Lemkul, You have written that I mix amber and charmm forcefields. It is kinda intiguing, becuase I downloaded lipid parameteres in amber and the atom names in the files are exactly the same as charmm-gui pdb output. Atom *names* in a coordinate file are an entirely different concept from atom *types* in a force field parameter set. I attach membrane pdb and parameter file. I would be very thankfull if you would take a look and judge if these are consistent. As I said - pdb2gmx worked well with these files, only grompp got troubles with "Unknown bond_atomtype CTL3". If CTL3 atom is characteristic for charmm ff why these names are used in amber files? I don't have nearly enough information to help you answer that question. But you've got an unknown atom type in your topology, that much is clear. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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
On 3/26/19 8:22 AM, vico...@fizyka.umk.pl 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. Where did I make mistake? It looks like you're mixing force fields between AMBER and CHARMM. CTL3 is a CHARMM atom type. You cannot mix force fields; you must develop the topology under a single, consistent parameter set. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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
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 .. > >> > > > > 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.
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.
Re: [gmx-users] grompp error: Unknown bond_atomtype
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? > 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.
[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.
