, 1950-58, 2010) 8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) 10: CHARMM36 all-atom force field (March 2017) 11: GROMOS96 43a1 force field 12: GROMOS96 43a2 force field (improved alkane dihedrals) 13: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 14: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 15: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 16: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9) 17: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 1 Using the Charmm36-jul2021 force field in directory ./charmm36-jul2021.ff Opening force field file ./charmm36-jul2021.ff/watermodels.dat Select the Water Model: 1: TIP3P_CHARMM CHARMM-modified TIP3P water model (recommended over original TIP3P) 2: TIP3P Original TIP3P water model 3: SPC SPC water model 4: SPCE SPC/E water model 5: TIP5P TIP5P water model 6: TIP4P TIP4P water model 7: TIP4PEW TIP4P/Ew water model 8: None 1 Opening force field file ./charmm36-jul2021.ff/aminoacids.r2b Opening force field file ./charmm36-jul2021.ff/carb.r2b Opening force field file ./charmm36-jul2021.ff/cgenff.r2b Opening force field file ./charmm36-jul2021.ff/ethers.r2b Opening force field file ./charmm36-jul2021.ff/lipid.r2b Opening force field file ./charmm36-jul2021.ff/metals.r2b Opening force field file ./charmm36-jul2021.ff/na.r2b Opening force field file ./charmm36-jul2021.ff/silicates.r2b Opening force field file ./charmm36-jul2021.ff/solvent.r2b Reading 3BLR.pdb... Read 2587 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 320 residues with 2587 atoms chain #res #atoms 1 'A' 320 2587 All occupancies are one Opening force field file ./charmm36-jul2021.ff/atomtypes.atp Atomtype 579 Reading residue database... (charmm36-jul2021) Opening force field file ./charmm36-jul2021.ff/aminoacids.rtp Residue 555 Sorting it all out... Opening force field file ./charmm36-jul2021.ff/carb.rtp Residue 918 Sorting it all out... Opening force field file ./charmm36-jul2021.ff/cgenff.rtp Residue 1786 Sorting it all out... Opening force field file ./charmm36-jul2021.ff/ethers.rtp Residue 1810 Sorting it all out... Opening force field file ./charmm36-jul2021.ff/lipid.rtp Residue 22210 Sorting it all out... Opening force field file ./charmm36-jul2021.ff/metals.rtp Residue 2228 Sorting it all out... Opening force field file ./charmm36-jul2021.ff/na.rtp Residue 2432 Sorting it all out... Opening force field file ./charmm36-jul2021.ff/silicates.rtp Residue 2437 Sorting it all out... Opening force field file ./charmm36-jul2021.ff/solvent.rtp Residue 2508 Sorting it all out... Opening force field file ./charmm36-jul2021.ff/aminoacids.hdb Opening force field file ./charmm36-jul2021.ff/carb.hdb Opening force field file ./charmm36-jul2021.ff/cgenff.hdb Opening force field file ./charmm36-jul2021.ff/ethers.hdb Opening force field file ./charmm36-jul2021.ff/lipid.hdb Opening force field file ./charmm36-jul2021.ff/metals.hdb Opening force field file ./charmm36-jul2021.ff/na.hdb Opening force field file ./charmm36-jul2021.ff/silicates.hdb Opening force field file ./charmm36-jul2021.ff/solvent.hdb Opening force field file ./charmm36-jul2021.ff/aminoacids.n.tdb Opening force field file ./charmm36-jul2021.ff/carb.n.tdb Opening force field file ./charmm36-jul2021.ff/cgenff.n.tdb Opening force field file ./charmm36-jul2021.ff/ethers.n.tdb Opening force field file ./charmm36-jul2021.ff/lipid.n.tdb Opening force field file ./charmm36-jul2021.ff/metals.n.tdb Opening force field file ./charmm36-jul2021.ff/na.n.tdb Opening force field file ./charmm36-jul2021.ff/silicates.n.tdb Opening force field file ./charmm36-jul2021.ff/solvent.n.tdb Opening force field file ./charmm36-jul2021.ff/aminoacids.c.tdb Opening force field file ./charmm36-jul2021.ff/carb.c.tdb Opening force field file ./charmm36-jul2021.ff/cgenff.c.tdb Opening force field file ./charmm36-jul2021.ff/ethers.c.tdb Opening force field file ./charmm36-jul2021.ff/lipid.c.tdb Opening force field file ./charmm36-jul2021.ff/metals.c.tdb Opening force field file ./charmm36-jul2021.ff/na.c.tdb Opening force field file ./charmm36-jul2021.ff/silicates.c.tdb Opening force field file ./charmm36-jul2021.ff/solvent.c.tdb Back Off! I just backed up topol.top to ./#topol.top.5# Processing chain 1 'A' (2587 atoms, 320 residues) Analysing hydrogen-bonding network for automated assignment of histidine protonation. 486 donors and 464 acceptors were found. There are 729 hydrogen bonds Will use HISD for residue 38 Will use HISE for residue 75 Will use HISE for residue 108 Will use HISE for residue 141 Will use HISE for residue 147 Will use HISE for residue 236 Will use HISE for residue 312 Identified residue SER7 as a starting terminus. Warning: Residue THP1186 in chain has different type (Other) from starting residue SER7 (Protein). Warning: Residue ASN187 in chain has different type (Protein) from starting residue SER7 (Protein). Warning: Residue ARG188 in chain has different type (Protein) from starting residue SER7 (Protein). Warning: Residue VAL189 in chain has different type (Protein) from starting residue SER7 (Protein). Warning: Residue VAL190 in chain has different type (Protein) from starting residue SER7 (Protein). More than 5 unidentified residues at end of chain - disabling further warnings. Identified residue TYR185 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS10 CYS13 HIS38 MET52 HIS75 CYS85 CYS95 SG26 SG50 NE2250 SD359 NE2551 SG629 SG711 CYS13 SG50 0.488 HIS38 NE2250 1.682 1.351 MET52 SD359 1.486 1.279 2.283 HIS75 NE2551 3.173 2.781 2.567 3.137 CYS85 SG629 1.104 0.666 0.774 1.535 2.499 CYS95 SG711 1.898 1.732 2.421 0.921 3.776 1.823 CYS106 SG801 2.741 2.263 1.734 2.513 1.358 1.749 2.869 HIS108 NE2820 3.662 3.179 2.465 3.182 2.330 2.597 3.258 MET130 SD989 4.222 3.761 3.479 3.627 1.660 3.382 4.077 MET132 SD1006 3.669 3.212 2.682 3.423 1.061 2.754 3.860 HIS141 NE21085 3.511 3.137 3.364 2.969 1.335 3.016 3.690 HIS147 NE21139 2.859 2.427 2.588 2.182 1.414 2.211 2.785 MET150 SD1165 3.339 2.904 2.964 2.657 1.386 2.657 3.232 CYS217 SG1697 4.327 3.890 3.924 3.395 2.351 3.629 3.841 MET219 SD1712 4.586 4.134 3.896 3.967 1.900 3.784 4.447 MET222 SD1734 4.161 3.682 3.295 3.521 1.915 3.242 3.855 MET229 SD1795 4.754 4.330 4.432 3.709 2.900 4.101 4.121 HIS236 NE21852 5.114 4.709 4.892 3.869 3.749 4.507 4.126 CYS245 SG1919 5.064 4.647 4.740 4.103 2.925 4.429 4.582 HIS312 NE22469 5.126 4.699 4.491 4.602 2.177 4.391 5.161 MET320 SD2541 5.035 4.598 4.036 4.801 1.987 4.167 5.274 CYS106 HIS108 MET130 MET132 HIS141 HIS147 MET150 SG801 NE2820 SD989 SD1006 NE21085 NE21139 SD1165 HIS108 NE2820 1.200 MET130 SD989 1.750 1.808 MET132 SD1006 1.065 1.481 1.046 HIS141 NE21085 2.011 2.743 1.501 1.778 HIS147 NE21139 1.273 2.003 1.514 1.556 1.018 MET150 SD1165 1.448 2.002 1.084 1.381 0.804 0.492 CYS217 SG1697 2.315 2.331 1.099 2.013 1.508 1.510 1.115 MET219 SD1712 2.174 2.213 0.438 1.394 1.580 1.819 1.345 MET222 SD1734 1.581 1.327 0.554 1.082 1.888 1.594 1.268 MET229 SD1795 2.858 2.775 1.603 2.567 1.938 2.001 1.645 HIS236 NE21852 3.465 3.205 2.469 3.367 2.775 2.634 2.401 CYS245 SG1919 3.115 3.103 1.643 2.656 1.926 2.250 1.831 HIS312 NE22469 2.820 2.969 1.216 1.906 1.852 2.422 1.948 MET320 SD2541 2.504 2.580 1.500 1.443 2.470 2.736 2.374 CYS217 MET219 MET222 MET229 HIS236 CYS245 HIS312 SG1697 SD1712 SD1734 SD1795 NE21852 SG1919 NE22469 MET219 SD1712 1.100 MET222 SD1734 1.239 0.909 MET229 SD1795 0.569 1.510 1.714 HIS236 NE21852 1.447 2.432 2.421 0.982 CYS245 SG1919 0.844 1.409 1.896 0.559 1.390 HIS312 NE22469 1.714 0.825 1.706 1.986 2.936 1.652 MET320 SD2541 2.521 1.434 1.757 2.938 3.833 2.775 1.320 Select start terminus type for SER-7 0: NH3+ 1: NH2 2: None Start terminus SER-7: NH3+ Select end terminus type for TYR-185 0: COO- 1: COOH 2: CT1 3: CT2 4: None 0 End terminus TYR-185: COO- Opening force field file ./charmm36-jul2021.ff/aminoacids.arn Checking for duplicate atoms.... Now there are 2586 atoms. Deleted 1 duplicates. Generating any missing hydrogen atoms and/or adding termini. Now there are 320 residues with 5228 atoms Making bonds... Number of bonds was 5281, now 5281 Generating angles, dihedrals and pairs... Before cleaning: 13904 pairs ------------------------------------------------------- Program gmx pdb2gmx, VERSION 5.1.4 Source code file: /home/chip/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/pgutil.c, line: 127 Fatal error: Residue 1 named GLY of a molecule in the input file was mapped to an entry in the topology database, but the atom N used in an interaction of type improper in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- [vicky@cys C9]$