Re: [gmx-users] Generating topology for a HEM protein with CHARMM27
On 5/25/16 9:58 AM, zeineb SI CHAIB wrote: @Justin, Thank you very much for your help, I finally fixed the problem but I'm having another one with grompp (which was expected): The error that I get is: ERROR 7 [file topol.top, line 41571]: No default Proper Dih. types Fatal error: There were 13 errors in input file(s) I think that the problem is about the bond parameters between SH in cystein and HEME iron group, isn't it? After looking in the literature, I found their corresponding parameters: I added the following fields in CHARMM file ffbonded.it: [ bondtypes ] ; i j func b0 kb SG FE1 0.232 209200.0 [ angletypes ] ; i j k functh0 cth ub0 cub CT2 SG FE 5 100.6 418.4 0.0 0.0 SG FE NPH 5 90.0 836.8 0.0 0.0 SG FE NPH 5 90.0 836.8 0.0 0.0 SG FE NPH 5 90.0 836.8 0.0 0.0 SG FE NPH 5 90.0 836.8 0.0 0.0 ; ### X CS SS X 9 0.200.0 3 CA CB SG FE 9 0.200.0 3 HB1 CB SG FE 9 0.200.0 3 HB1 CB SG FE 9 0.200.0 3 ; ### X FE SS X 9 0.000.0 4 CB SG FE NPH 9 0.000.0 4 CB SG FE NPH 9 0.000.0 4 CB SG FE NPH 9 0.000.0 4 But after that, I had another type of error: Fatal error: Unknown bond_atomtype SG I added an SG entry in atomtypes.atp but I'm having the same error? Am I missing something? SG is an atom *name*, not an atom *type*. atomtypes.atp is also irrelevant anyway, as it is only read by pdb2gmx, so that's not how you add new atom types. But in any case, this is not what you should be doing anyway. Be careful that your protonation states are correct - make sure that -SH is correct (instead of the thiolate form) before adding a bunch of parameters and trying to do the simulation. -Justin Thank you very much for all your help and guidance Justin! Regards. Zeineb. From: zeineb...@hotmail.com To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Generating topology for a HEM protein with CHARMM27 Date: Mon, 23 May 2016 10:31:05 +0100 I'm looking to generate the topology of a HEM protein , I choose CHARMM as a force field. At the begining, when I run pdb2gmx I had this error about missing hydrogen's: WARNING: atom HA is missing in residue HEM 473 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 473 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) --- Program pdb2gmx, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/kernel/pdb2top.c, line: 1588 Fatal error: There were 30 missing atoms in molecule Other2, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- After a research, I found what was missing: I made a copy of aminoacids.hdb (Charmm27.ff folder) in my working directory and I edited this file: I added the following Lines: HEME 16 1 1 HA CHA C1A C4D 1 1 HB CHB C4A C1B 1 1 HC CHC C1C C4B 1 1 HD CHD C1D C4C 3 4 HMA CMA C3A C2A 2 6 HAA CAA C2A CBA 2 6 HBA CBA CAA CGA 3 4 HMB CMB C2B C1B 1 1 HAB CAB C3B CBB 2 3 HBB CBB CAB C3B 3 4 HMC CMC C2C C1C 1 1 HAC CAC CBC C3C 2 3 HBC CBC CAC C3C 3 4 HMD CMD C2D C1D 2 6 HAD CAD C2D CBD 2 6 HBD CBD CAD CGD I fixed the problem of missing hydrogens but I'm having another type of error: Special Atom Distance matrix: HEM360 HEM360 CAB2CAC3 HEM360CAC3 0.796 HEM360FE43 0.557 0.557 --- Program gmx pdb2gmx, VERSION 5.1.2 Source code file: /home/francois/Bureau/Zineb/gromacs-5.1.2/src/gromacs/gmxpreprocess/resall.c, line: 645 Fatal error: Residue 'HEM' not found in residue topology database For more information and tips
Re: [gmx-users] Generating topology for a HEM protein with CHARMM27
@Justin, Thank you very much for your help, I finally fixed the problem but I'm having another one with grompp (which was expected): The error that I get is: ERROR 7 [file topol.top, line 41571]: No default Proper Dih. types Fatal error: There were 13 errors in input file(s) I think that the problem is about the bond parameters between SH in cystein and HEME iron group, isn't it? After looking in the literature, I found their corresponding parameters: I added the following fields in CHARMM file ffbonded.it: [ bondtypes ] ; i j func b0 kb SG FE1 0.232 209200.0 [ angletypes ] ; i j k functh0 cth ub0 cub CT2 SG FE 5 100.6 418.4 0.0 0.0 SG FE NPH 5 90.0 836.8 0.0 0.0 SG FE NPH 5 90.0 836.8 0.0 0.0 SG FE NPH 5 90.0 836.8 0.0 0.0 SG FE NPH 5 90.0 836.8 0.0 0.0 ; ### X CS SS X 9 0.200.0 3 CA CB SG FE 9 0.200.0 3 HB1 CB SG FE 9 0.200.0 3 HB1 CB SG FE 9 0.200.0 3 ; ### X FE SS X 9 0.000.0 4 CB SG FE NPH 9 0.000.0 4 CB SG FE NPH 9 0.000.0 4 CB SG FE NPH 9 0.000.0 4 But after that, I had another type of error: Fatal error: Unknown bond_atomtype SG I added an SG entry in atomtypes.atp but I'm having the same error? Am I missing something? Thank you very much for all your help and guidance Justin! Regards. Zeineb. From: zeineb...@hotmail.com To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Generating topology for a HEM protein with CHARMM27 Date: Mon, 23 May 2016 10:31:05 +0100 I'm looking to generate the topology of a HEM protein , I choose CHARMM as a force field. At the begining, when I run pdb2gmx I had this error about missing hydrogen's: WARNING: atom HA is missing in residue HEM 473 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 473 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) --- Program pdb2gmx, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/kernel/pdb2top.c, line: 1588 Fatal error: There were 30 missing atoms in molecule Other2, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- After a research, I found what was missing: I made a copy of aminoacids.hdb (Charmm27.ff folder) in my working directory and I edited this file: I added the following Lines: HEME 16 1 1 HA CHA C1A C4D 1 1 HB CHB C4A C1B 1 1 HC CHC C1C C4B 1 1 HD CHD C1D C4C 3 4 HMA CMA C3A C2A 2 6 HAA CAA C2A CBA 2 6 HBA CBA CAA CGA 3 4 HMB CMB C2B C1B 1 1 HAB CAB C3B CBB 2 3 HBB CBB CAB C3B 3 4 HMC CMC C2C C1C 1 1 HAC CAC CBC C3C 2 3 HBC CBC CAC C3C 3 4 HMD CMD C2D C1D 2 6 HAD CAD C2D CBD 2 6 HBD CBD CAD CGD I fixed the problem of missing hydrogens but I'm having another type of error: Special Atom Distance matrix: HEM360 HEM360 CAB2CAC3 HEM360CAC3 0.796 HEM360FE43 0.557 0.557 --- Program gmx pdb2gmx, VERSION 5.1.2 Source code file: /home/francois/Bureau/Zineb/gromacs-5.1.2/src/gromacs/gmxpreprocess/resall.c, line: 645 Fatal error: Residue 'HEM' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I added an entry in residuetype.dat (HEM Protein), after making a copy in my working directory but it didn't fix the problem. I verified each file and they seem OK, I can't find where is the problem!!! Any help please!!! Kind regards. Zeineb.
Re: [gmx-users] Generating topology for a HEM protein with CHARMM27
On 5/23/16 5:31 AM, zeineb SI CHAIB wrote: I'm looking to generate the topology of a HEM protein , I choose CHARMM as a force field. At the begining, when I run pdb2gmx I had this error about missing hydrogen's: WARNING: atom HA is missing in residue HEM 473 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 473 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) --- Program pdb2gmx, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/kernel/pdb2top.c, line: 1588 Fatal error: There were 30 missing atoms in molecule Other2, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- After a research, I found what was missing: I made a copy of aminoacids.hdb (Charmm27.ff folder) in my working directory and I edited this file: I added the following Lines: The .hdb file must still be in the force field directory (wherever that may be, $GMXLIB or working directory), not in the working directory itself. Otherwise it will have no effect. HEME 16 1 1 HA CHA C1A C4D 1 1 HB CHB C4A C1B 1 1 HC CHC C1C C4B 1 1 HD CHD C1D C4C 3 4 HMA CMA C3A C2A 2 6 HAA CAA C2A CBA 2 6 HBA CBA CAA CGA 3 4 HMB CMB C2B C1B 1 1 HAB CAB C3B CBB 2 3 HBB CBB CAB C3B 3 4 HMC CMC C2C C1C 1 1 HAC CAC CBC C3C 2 3 HBC CBC CAC C3C 3 4 HMD CMD C2D C1D 2 6 HAD CAD C2D CBD 2 6 HBD CBD CAD CGD I fixed the problem of missing hydrogens but I'm having another type of error: Special Atom Distance matrix: HEM360 HEM360 CAB2CAC3 HEM360CAC3 0.796 HEM360FE43 0.557 0.557 --- Program gmx pdb2gmx, VERSION 5.1.2 Source code file: /home/francois/Bureau/Zineb/gromacs-5.1.2/src/gromacs/gmxpreprocess/resall.c, line: 645 Fatal error: Residue 'HEM' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I added an entry in residuetype.dat (HEM Protein), after making a copy in my working directory but it didn't fix the problem. I verified each file and they seem OK, I can't find where is the problem!!! Any help please!!! The residue name is HEME, not HEM (specbond.dat changes it). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Generating topology for a HEM protein with CHARMM27
I'm looking to generate the topology of a HEM protein , I choose CHARMM as a force field. At the begining, when I run pdb2gmx I had this error about missing hydrogen's: WARNING: atom HA is missing in residue HEM 473 in the pdb file You might need to add atom HA to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) WARNING: atom HB is missing in residue HEM 473 in the pdb file You might need to add atom HB to the hydrogen database of building block HEME in the file aminoacids.hdb (see the manual) --- Program pdb2gmx, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/kernel/pdb2top.c, line: 1588 Fatal error: There were 30 missing atoms in molecule Other2, if you want to use this incomplete topology anyhow, use the option -missing For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- After a research, I found what was missing: I made a copy of aminoacids.hdb (Charmm27.ff folder) in my working directory and I edited this file: I added the following Lines: HEME 16 1 1 HA CHA C1A C4D 1 1 HB CHB C4A C1B 1 1 HC CHC C1C C4B 1 1 HD CHD C1D C4C 3 4 HMA CMA C3A C2A 2 6 HAA CAA C2A CBA 2 6 HBA CBA CAA CGA 3 4 HMB CMB C2B C1B 1 1 HAB CAB C3B CBB 2 3 HBB CBB CAB C3B 3 4 HMC CMC C2C C1C 1 1 HAC CAC CBC C3C 2 3 HBC CBC CAC C3C 3 4 HMD CMD C2D C1D 2 6 HAD CAD C2D CBD 2 6 HBD CBD CAD CGD I fixed the problem of missing hydrogens but I'm having another type of error: Special Atom Distance matrix: HEM360 HEM360 CAB2CAC3 HEM360CAC3 0.796 HEM360FE43 0.557 0.557 --- Program gmx pdb2gmx, VERSION 5.1.2 Source code file: /home/francois/Bureau/Zineb/gromacs-5.1.2/src/gromacs/gmxpreprocess/resall.c, line: 645 Fatal error: Residue 'HEM' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I added an entry in residuetype.dat (HEM Protein), after making a copy in my working directory but it didn't fix the problem. I verified each file and they seem OK, I can't find where is the problem!!! Any help please!!! Kind regards. Zeineb. -- 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] Generating topology for a hem protein
On 5/19/16 9:41 AM, zeineb SI CHAIB wrote: Dear all, I'm desperetly looking for help to generate the topology of my hem protein. I'm using CHARMM as a force field and apparently PDB2gmx assigns dihedrals that should not exist and it's complicated to verify everything. Justin suggested using CHARMM-GUI, I followed a tutorial that I found on line (http://cermm.concordia.ca/workshopDocs/CHARMM/Lague.pdf) in order to build my system, I'm in the final step, adding the Hem group to my protein but I don't know how to do it and I don't know if all the steps went well or not. If you don't know, how can anyone on this list know? If something went wrong with CHARMM-GUI, there would be a fatal error. It's as simple as uploading the PDB file and letting CHARMM-GUI do the work; our latest version even writes all the GROMACS topologies and input files for you. It will generate the correct dihedrals for heme groups. Unless you can provide a specific issue (with GROMACS, because this is not the place for CHARMM-GUI problems), there's nothing anyone can do to help you. We can't guess what the problem is, and in this instance, you haven't even said if there is a problem. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Generating topology for a hem protein
Dear all, I'm desperetly looking for help to generate the topology of my hem protein. I'm using CHARMM as a force field and apparently PDB2gmx assigns dihedrals that should not exist and it's complicated to verify everything. Justin suggested using CHARMM-GUI, I followed a tutorial that I found on line (http://cermm.concordia.ca/workshopDocs/CHARMM/Lague.pdf) in order to build my system, I'm in the final step, adding the Hem group to my protein but I don't know how to do it and I don't know if all the steps went well or not. Any advices, HELP please!! I'll really appreciate your help, time and patience! Regards. Zeinbe. -- 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] Generating topology for a HEM protein with CHARMM27
@ Justin Dear Justin, Thank you very much for your orientation and help. I visited CHARMM-GUI website and I found interesting tutorials for my HEM-protein but before going further I would like to know if it's feasible to use CHARMM GUI for my Hem-Protein and include after my substrate (amino-acide) and a cofactor (Tetrahydrofolat) If yes, How can I do it? Any advices, tipes? After all, my goal is to simulate this hole system on GROMACS. NB: I also have problems with generating the topology of tetrahydrofolate from the website that you recommended 'https://cgenff.paramchem.org/initguess/#20160513/THF_zinc_4228237.str' in a another post and I just added a comment)). Thank you very much for your help. Zeineb. -- 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] Generating topology for a HEM protein with CHARMM27
Dear gmx users, I'm working on simulating a homodimer with its cofactors (hem, THG) and its substrate with GROMACS. Since my system is complex, I decided to start first with a monomere taking only protein residues and the hem group. When I run pdb2gmx, using CHARMM27 FF, I had this error: "Fatal error: There were 30 missing atoms in molecule Other_chain_A, if you want to use this incomplete topology anyhow, use the option -missing"! I think that this error is about hydrogen atoms but since my PDB is generated by X-RAY diffraction there is no hydrogen! What should I so? Thank you in advance for your help. Zineb. -- 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.
