The program INTOCHAM converts a structure file (.car file) produced by InsightII into any of the followings:
At start, the program will quiz you about the conversion type (Insight to Quanta or to Charmm 2.2, Insight to Amber with or without potential conversion, Insight to Moil, back from Charmm to Insight).
For conversions from Insight, the program will ask the following information:
After the type conversion, you have the option to change the new type of any of the atoms (i.e., override the program's 'judgement') - a must when no conversion has been assigned by the program. It is important that any such change be made at this point because the choice of improper torsion terms in Charmm depends on the types of the atoms and changing atomtypes after the improper torsion terms are selected may result in missing some of them. Thus if messages about ambiguous or missing conversions were received, the conversion may have to be repeated. After having examined the structure with this list in hand one can decide about the necessary changes. The new atomnames can be identified with their original sequence numbers by looking at the generated Charmm COOR file.
The program also gives you the option to switch to united atom representation of the carbons (with CVFF input only). In this case hydrogens bonded to carbons are dropped, and the atomtypes of the corresponding carbons are changed to the respective united atom types. Also, the hydrogen charges are added to that of the carbon. Conversions to Charmm convert only the aliphatic carbons. Conversions to Amber converts all aromatic carbons to type CD. Note, however that the Amber force field contains several different aromatic carbon atomtypes (CD, CE, CF, CG, CI, CJ, CP) depending on the environment of the united atom.
The program will recognize different molecules as separate residues. The residue name of the molecule will be the residue name given by Insight to the first atom (see Amber groupings below, though). Thus, if you want to control the Charmm residue names, you have to edit the Residue ID field of the .car file (columns 52-55). If two molecules have the same residue name and their chemical formula is probably the same (the sum of the atomic number squares are the same) then the conversion assumes the second molecule to have the same description as the first and will not make any entry into the Charmm RTF file. The program will give the number of molecules found to be duplicates in this sense. If two different molecules were given the same residue name then the program will ask you to type in a new residue name for the second molecule.
The group concept, important when large molecules are modeled because the cutoffs can be based on the groups and not on the whole molecule, is also implemented. Groups can be defined by Insight (Builder/Forcefield/Groups). Alternatively, you can also request the converter to treat the different Insight-defined residues as different groups. Conversions to Charmm will translate it into grouping of the atoms within the residues using the GROUP command in the RTF input. Conversions to Amber or Moil, on the other hand, will create a separate 'molecule' (monomer in the Moil terminology) for each group in the actual molecule and provide the inter-group bonds as 'crosslinks' (for Amber) or additional bonds specified in the addbond file (for Moil). If the Insight-defined grouping is invoked, the .mdf file corresponfing to the .car file has to be available as well.
The program assumes that residues named WTR are solvents and treats them accordingly. You will be quizzed if you used an other solvent name.
If periodic boundary conditions were used by Insight, the conversion to Charmm will implement them too. In this case, you will be quizzed about the location of the Charmm image file (default provided). The box size is also written on the message file. Note that the Insight box has the origin of the coordinate system at a vertex of the simulation cell.
The atoms will be printed in an order that puts the solvent molecules at the end. If the solute was also found to consist of disconnected parts (separate molecules) or the atoms were grouped according to the Insight residues then the order of the atoms in the Charmm COOR file will put atoms in the same group/molecule consecutively. The program will write the information about this resequencing of the atoms in the structure into a file whose name is generated from the .car file, with .car replaced by .seq : for each input atom it gives its new sequence number. This file is also needed later if a Charmm COOR file is to be converted back to Insight. Also, the Charmm COOR file generated will have the old sequence number in its first column.
The input file to Charmm will have the same name as the Insight .car file, except that the extension .car will be replaced by .ch . The Amber files will have extensions .prep , .link and .edit (for the unit 5 inputs of the programs PREP, LINK and EDIT, respectively) and .pdbin and .addwat for the coordinate files for the solute and solvents (if any), respectively.
In addition, the program also writes to any conversion-related message and an annotated list of the improper torsions generated to a message file whose name is derived from the Insight .car file name by replacing the extension with .msg . It is suggested that the user review this list.
The Charmm input file will contain in the title the Insight file name, the list of conversions employed originally and the name of the parameter file used. It will include into the RTF file all improper torsions for which the parameter file contained an entry, but will limit to one the number of improper torsion terms centered on any given atom and will reject a parameter file entry that would make the environment of a four-bonded carbon planar. There will be no IC (internal coordinate) entries - they are not needed since a complete coordinate file is given. The last Charmm command is a steepest descent minimization with default parameters.
The result of the conversion can be submitted to Charmm as is and should, in principle, run through without fatal error. A possible problem is that potential parameters are missing. This can be either the result of the shortcoming of the parameter file or an incorrect conversion built into the program. Once the converted Charmm input file has been found free of errors, the actual Charmm commands performing calculations and saving the results can be added manually.
The Amber input files are annotated at the end with reference to the conversion program. The PREP input also describes the conversions used.
For conversion from Charmm back to Insight the program asks the name of the Insight .car file, the name of the Charmm .CRD file and the name to be given to the new Insight .car file.
ERROR messages can indicate problems with the data or insufficient capacity. In case of the latter, the dimensions of the program should be increased. Any message prefixed with PROGRAM ERROR indicates an internal inconsistency likely due to a program error and should be reported to the author.
Charmm and Amber atomtypes assigned to Insight (CVFF) atomtypes Conv. CVFF -> CHARMm CHARMM AMBER num. Quanta V 2.2 1 h HA HA HC 2 d HA HA 3 hn H (a) HC H HC (c) H 4 ho H (a) H HO HC (b) 5 hp H (a) H HC (b) 6 hs H (a) H HS HC (b) 7 h* HT HT HO 8 c CH3E CT1 CT 84: CT2 85: CT3 9 cg CT C2 CT 10 c' C C C 11 cp C6R (d) CA CA 90: CR66 94: CR 91: CR56 12 cr C CA CA 13 c- C (?) C (?) 14 ca CT CT1 CT 15 c3 CT CT3 CT 16 cn CT CT1 CT 86: CT2 17 c2 CT CT CT 18 c1 CT CT2 CT 19 c5 C5R (d) CA C* 88: CR55 92: CC 89: CR56 93: CB 20 c= CUA1 (e) C (?) 21 ct CUY1 (f) 22 ci C5R (?) CA (?) 23 n NP NH2 N 24 n2 NT 25 np N6R (g) NC 87: N5R (h) 26 n3 NT NN5 N3 27 n4 NT NT 28 n= 29 nt 30 n1 NC 31 ni NC (?) NR3 32 o' O O1 O 81: OA 83: OB 82: OK 33 o OS OS OS 34 o- OC OC 35 oh OT OH OH 36 o* OW (i) OT OH 37 s SE 38 s1 ST S 39 sh ST SH 40 p PT P 41 si MSI 42 f XF 43 cl XCL 44 br XBR 45 Cl XCL 46 Na MNA 47 c+ 48 nu 98 United atom CH1 CH1E CH 99 United atom CH2 CH2E C2 100 United atom CH3 CH3E C3 ------------------------------------------------------------------- a: neutral; b: purines/pyrimidines c: charged d: see also CR55,CR56,CR66,C5RP,C6RP g: 6-membered ring; h: 5-membered ring e: see also CUA2 i: TIP3P water (OH2 for ST2) f: see also CUY2, CUY3 ?: Weak correspondence
CVFF force field atom types Atom Type Description 1 h Hydrogen bonded to C. 2 d General Deuterium. 3 hn Hydrogen bonded to N. 4 ho Hydrogen bonded to O. 5 hp Hydrogen bonded to P. 6 hs Hydrogen bonded to S. 7 h* Hydrogen in water molecule. 8 c sp3 aliphatic carbon. 9 cg sp3 alpha carbon in glycine. 10 c' sp2 carbon in carbonyl (C=O) group. 11 cp sp2 aromatic carbon (partial double bonds). 12 cr Carbon in guanidinium group (HN=C(NH2)2). 13 c- Carbon in charged carboxylate (COO-) group. 14 ca General amino acid alpha carbon (sp3). 15 c3 sp3 carbon in methyl (CH3) group. 16 cn sp3 carbon bonded to N. 17 c2 sp3 carbon bonded to 2 H's, 2 heavy atoms. 18 c1 sp3 carbon bonded to 1 H, 3 Heavy atoms. 19 c5 sp2 aromatic carbon in five membered ring. 20 c= sp2 nonaromatic carbon involved in double bond. 21 Ct sp carbon involved in triple bond. 22 ci Aromatic carbon in a charged imidazole ring (HIS+). 23 n sp2 nitrogen with 1 H, 2 heavy atoms (amide group). 24 n2 sp2 nitrogen (NH2 in the guanidinium group (HN=C(NH2)2). 25 np sp2 aromatic nitrogen (partial double bond) 26 n3 sp3 nitrogen with three substituents. 27 n4 sp3 nitrogen with four substituents. 28 n= sp2 nitrogen involved in a double bond (non-aromatic). 29 nt sp nitrogen involved in triple bond. 30 n1 sp2 nitrogen in charged arginine. 31 ni sp2 nitrogen in a charged imidazole ring (HIS+). 32 o' Oxygen in carbonyl (C=O) group. 33 o sp3 oxygen in ether or ester groups. 34 o- Oxygen in charged carboxylate (COO-) group. 35 oh Oxygen in hydroxyl (OH) group. 36 o* Oxygen in water molecule. 37 s Sulfur in methionine (C-S-C) group. 38 s1 Sulfur involved in S-S disulfide bond. 39 sh Sulfur in sulfhydryl (-SH) group. 40 p General phosphorous atom. 41 si Silicon. 42 f Fluorine bonded to a carbon. 43 cl Chlorine bonded to a carbon. 44 br Bromine bonded to a carbon. 45 Cl Chloride ion. 46 Na Sodium ion. 47 c+ Calcium ion-Ca++ 48 nu NULL atom for relative free energy.
CHARMm atomtypes from Quanta parameter file 1 H Hydrogen bonding hydrogen (neutral group) 2 HC Hydrogen bonding hydrogen (charged group) 3 HA Aliphatic or aromatic hydrogen 4 HT TIPS3P water model hydrogen 5 LP ST2 lone pair 6 BE Beryllium 7 B Boron 10 CT Aliphatic carbon (tetrahedral) 11 CH1E Extended atom carbon with one hydrogen 12 CH2E Extended atom carbon with two hydrogens 13 CH3E Extended atom carbon with three hydrogens 14 C Carbonyl or Guanidinium carbon 15 CM Carbonmonoxide carbon 16 CUA1 Carbon in double bond,first pair 17 CUA2 Carbon in double bond,second pair conjd.to first 18 CUY1 Carbon in triple bond,first pair 19 CUY2 Carbon in triple bond,second pair 21 C5R Aromatic carbon in a five member ring 22 C6R Aromatic carbon in a six member ring 23 C5RE Extended aromatic carbon in five member ring 24 C6RE Extended aromatic carbon in six member ring 25 CR55 Aromatic carbon-merged five member rings 26 CR56 Aromatic carbon-merged five/six member rings 27 CR66 Aromatic carbon-merged six member rings 28 C5RP for Aryl-Aryl bond between C5R rings 29 C6RP for Aryl-Aryl bond between C6R rings 30 N5RP Nitrogen for bridghead between 5-mem rings 31 N Nitrile nitrogen 32 NP Peptide/amide nitrogen 33 NX Proline nitrogen 34 N5R Nitrogen in a five member aromatic ring 35 N6R Nitrogen in a six member aromatic ring 36 NT Amine nitrogen (tetrahedral) 37 NC Charged guanidinuim nitrogen 38 NO2 Nitro group nitrogen 40 O Carbonyl oxygen for amides 41 OA Carbonyl oxygen for aldehydes 42 OK Carbonyl oxygen for ketones 43 OC Charged oxygen 45 OT Hydroxyl oxygen (tetrahedral)/Ionizable acid oxygen 46 OW TIP3P water model oxygen 47 OH2 ST2 water model oxygen 48 OM Carbonmonoxide oxygen 49 OS Ester oxygen 50 OE Ether oxygen / Acetal oxygen 51 OAC Carbonyl oxygen for acids 52 O5R Oxygen in five member aromatic ring 60 PT Phosphorous (tetrahedral) 61 PO3 Phosphorous bonded to three oxygens 62 PO4 Phosphorous bonded to four oxygens 70 ST Sulphur (tetrahedral) 71 SH1E Extended atom sulphur with one hydrogen 72 S5R Sulphur in a five member aromatic ring 73 S6R Thioether sulphur 74 SE Thiocarbonyl sulphur 75 SK Thioketone sulphur 76 SO1 Sulphur bonded to one oxygen 77 SO2 Sulphur bonded to two oxygens 78 SO3 Sulphur bonded to three oxygens 79 SO4 Sulphur bonded to four oxygens 80 MLI Lithium 81 MNA Sodium 82 MMG Magnesiun 83 MK Potassium 84 MCA Calcium 85 MMN Manganese 86 MFE Iron 87 MZN Zinc 88 MRB Rubidium 89 MCS Cesium 90 MSI Silicon 91 MAL ALuminum 92 XF Fluorine 93 XCL Chlorine 94 XBR Bromine 95 XI Iodine 96 MCU Copper 97 MV Vanadium 98 MCR Chromium 99 MCO Cobalt 100 MNI Nickel 101 MAS Arsenic 102 MSE Selenium 103 MSR Strontium 104 MY Yttrium 105 MZR Zirconium 106 MNB Niobium 107 MMO Molybdenum 108 MRU Ruthenium 109 MRH Rhodium 110 MPD Palladium 111 MAG Silver 112 MCD Cadmium 113 MSN Tin 114 MSB Antimony 115 MBA Barium 116 MW Tungsten 117 MOS Osmium 118 MPT Platinum 119 MAU Gold 120 MHG Mercury 121 MPB Lead 122 MBI Bismuth 123 MLA Lanthanum 124 MCE Cerium 125 MPR Praseodymium 126 MAC Actinium 127 MTH Thorium 128 MU Uranium 129 MTE Tellurium 130 MPO Polonium 131 AT Astatine 132 MTC Technetium 133 MSC Scandium 134 MTI Titanium 135 MGA Gallium 136 MGE Germanium 137 MIN Indium 138 MHF Hafnium 139 MTA Tantalum 140 MIR Iridium 141 MTL Thallium 142 MFR Francium 143 MRA Radium 144 MND Neodymium 145 MPM Promethium 146 MSM Samarium 147 MEU Europium 148 MGD Gadolinium 149 MTB Terbium 150 MDY Dysprosium 151 MHO Holmium 152 MER Erbium 153 MTM Thulium 154 MYB Ytterbium 155 MLU Lutetium 156 MPA Protactinium 157 MNP Neptunium 158 MPU Plutonium 159 MAM Americium 160 MCM Curium 161 MBK Berkelium 162 MCF Californium 163 MES Einsteinium 164 MFM Fermium 165 MMD Medelevium 166 MNO Nobelium 167 MLR Lawrencium 168 HE Helium 169 NE Neon 170 AR Argon 171 KR Krypton 172 XE Xenon 173 RN Radon
Charmm 2.2 atomtypes (from the protein parameter file) 1 H polar H 2 HC N-ter H 3 HA nonpolar H 4 HT TIPS3P WATER HYDROGEN 5 HP aromatic H 6 HB backbone H 7 HR1 his he1, (+) his HG,HD2 8 HR2 (+) his HE1 9 HR3 neutral his HG, HD2 11 C carbonyl C, peptide backbone 12 CA aromatic C 13 CT1 aliphatic sp3 C for CH 14 CT2 aliphatic sp3 C for CH2 15 CT3 aliphatic sp3 C for CH3 16 CPH1 his CG and CD2 carbons 17 CPH2 his CE1 carbon 18 CPT trp C between rings 19 CY TRP C in pyrrole ring 20 CP1 tetrahedral C (proline CA) 21 CP2 tetrahedral C (proline CB/CG) 22 CP3 tetrahedral C (proline CD) 23 CC carbonyl C, asn,asp,gln,glu,cter,ct2 24 CD carbonyl C, pres aspp,glup,ct1 25 CPA heme alpha-C 26 CPB heme beta-C 27 CPM heme meso-C 28 CM heme CO carbon 29 CS thiolate carbon 31 N proline N 32 NR1 neutral his protonated ring nitrogen 33 NR2 neutral his unprotonated ring nitrogen 34 NR3 charged his ring nitrogen 35 NH1 peptide nitrogen 36 NH2 amide nitrogen 37 NH3 ammonium nitrogen 38 NC2 guanidinium nitroogen 39 NY TRP N in pyrrole ring 40 NP Proline ring NH2+ (N-terminal) 41 NPH heme pyrrole N 51 O carbonyl oxygen 52 OB carbonyl oxygen in acetic acid 53 OC carboxylate oxygen 54 OH1 hydroxyl oxygen 55 OS ester oxygen 56 OT TIPS3P WATER OXYGEN 57 OM heme CO/O2 oxygen 81 S sulphur 82 SM sulfur C-S-S-C type 83 SS thiolate sulfur 90 CAL calcium 2+ 91 ZN zinc (II) cation 92 FE heme iron 56