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 CAB2 CAC3 HEM360 CAC3 0.796 HEM360 FE43 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.