C C i_RESP version 3.1 November 30th, 2104. C q4md-forcefieldtools.org C Increase the limits of the program (maxq, maxlgr, maxmol, etc...) C 'nmol' is replaced by 'nmep' in the inputs C Format i5,i6 for the 1st line of Unit 10 (espot file) C and for the esp.qm-induced file C Blank line whatever the number of structure(s) "nmep" is C before the use intra-molecular charge constraint C C i_RESP version 3.0 February 2009-Jan 2011, Piotr Cieplak C iterated-RESP for taking into account polarization c effects. Program is an extension of the original c RESP program C RESP version 2.1 October 1994 Jim Caldwell C RESP version 2.0 September 1992 C Author: Christopher Bayly C ESPFIT version 1.0 modified by Ian Gould to run in conjunction C with gaussian 90. C ESPFIT version 1.0 (G80UCSF): C U.CHANDRA SINGH AND P.A.KOLLMAN C C All authors: C C DEPARTMENT OF PHARMACEUTICAL CHEMISTRY C SCHOOL OF PHARMACY C UNIVERSITY OF CALIFORNIA C SAN FRANCISCO CA 94143 C C Piotr Cieplak - currently: C Sanford|Burnham Medical Research Institute, C La Jolla, CA 92037 C C--------------------------------------------------------------------- C C Versions 1.0-2.1: C THIS PROGRAM FITS THE QUANTUM MECHANICALLY CALCULATED C POTENTIAL AT MOLECULAR SURFACES USING AN ATOM-CENTERED C POINT CHARGE MODEL. THE MOLECULAR SURFACES ARE GENERATED C BEYOND VAN DER WAALS SURFACE IN ORDER TO MINIMIZE OTHER C CONTRIBUTIONS SUCH AS EXCHANGE REPULSION AND CHARGE TRANSFER C C Version 3.0 - Program capable of fitting charges for polarizable force C fields. It allows for fitting charges to effective C electrostatic potential that is a difference between quantum C mechanically derived electrostatic potential and the one C produced by induced dipoles. In order to take into account C the effects associated with self polarization of a molecule C due to induced dipoles - this fitting is done iteratively. C The i_RESP program maintains its full capabilities of C standard RESP program C C Aug, 2012: C Updated: the formula for quadrupole moment is corrected C (traceless formula) c Feb 20,2013 c Updated: print the dipole and quadrupole moments reoriented c according to principal components analysis and center of mass C C--------------------------------------------------------------------- C C -1st- TITLE FORMAT(10A8) C C--------------------------------------------------------------------- C c -2nd- C C OPTIONS FOR THE JOB begin with " &cntrl" c end with " &end" c note leading blanks !!!!!!!!!! C C C INOPT = 0 ... NORMAL RUN C = 1 ... CYCLE THROUGH A LIST OF DIFFERENT qwt c read from -w unit c C IOUTOPT = 0 NORMAL RUN C = 1 write restart info of new esp etc to c unit -e (esout unit) C C IQOPT = 0 ... use the q's which are read from the -i unit C = 1 ... RESET ALL INITIAL CHARGES TO ZERO C = 2 ... READ IN NEW INITIAL CHARGES FROM -q (qwt) C = 3 ... READ IN NEW INITIAL CHARGES FROM -q (qwt) C AND PERFORM AVERAGING OF THOSE NEW C INITIAL CHARGES ACCORDING TO IVARY VALUES C C NMEP = the number of Molecular Electrostatic Potential(s) (MEP) in a multiple MEP fit (default 1) C MEP(s) = orientation(s), conformation(s) or molecule(s) C C ihfree = 0 ... ALL ATOMS ARE RESTRAINED C = 1 ... HYDROGENS NOT RESTRAINED C C irstrnt = 0 ... HARMONIC RESTRAINTS (old style) C = 1 ... HYPERBOLIC RESTRAINT TO CHARGE OF ZERO (default) C = 2 ... ONLY ANALYSIS OF INPUT CHARGES; C NO CHARGE FITTING IS CARRIED OUT c c iunits = 0 ... atom coordinates in angstroms c = 1 " " " bohrs c (this option is inactive - input coordinates c and esp's are read as having a.u. units) c c c qwt = restraint weight if irstrnt = 1 c c- - - - - - c Additional set of input parameters for polarizable charge fitting in i_resp: c c ipol = 0 standard RESP fitting (default) c = 1 iterated RESP, Applequist - type polarizability model(3) c = 2 iterated RESP, Amoeba type Thole screening, acc.to Ren, c Ponder (model 3) c = 3 iterated RESP, Thole-exponential type polarizability c model(2) c = 4 iterated RESP, Thole-linear type polarizability model(1) c = 5 iterated RESP, Gaussian - type polarizability model c Elking, Ponder et al. (not incorporated yet) c c If ipol.ne.0 - atomic polarizabilities must be read-in c from external file. Units - a.u. (???) c The values of polarizabilities depend on the ipol model c Program tries to assign polarizabilities to atoms based on c atom types/connectivities. c Alternatively - the actual atomic polarizabilities, already c assigned to atoms by user can be read from the cards defining c IVARY for each unique center, see -6th- cards description. c c If ipol.ne.0 then the read-in ESP's for each molecule c will be initially "iterated" before performing c multimolecule or multiconformational and restrained c fitting c c ipol_iter = N number of iterations for obtaining polarized, c "iterated" R/ESP charges c (default N=30) c c ilp = 0 - do not add lone pairs/extra-interacting-points to c electron donating atoms c = 1 - add additional lone pairs/extra points before charge fitting c ??? take care of putting zero polarizabilities c ??? and proper handling 1-4,1-3,1-2 interactions c ??? this option is not active yet c c ???check it (it should not be for Applequist only for now): c ??????? Parameters below are for Applequist polarization model only, c since 1-2 and 1-3 interactions are excluded, and 1-4 are scaled by scee c In the Thole models - all interactions are included, e.g. all point c dipoles see all other point dipoles. c c n12 = 0 exclude 1-2 interactions in polarized charge fitting c (default for Applequist model) c = 1 include 1-2 interactions. c n13 = 0 exclude 1-3 interactions in polarized charge fitting c (default for Applequist model) c = 1 include 1-3 interactions. c n14 = 0 exclude 1-4 interactions in polarized charge fitting c = 1 include 1-4 interactions (default for Applequist and other models). c c SCEE = 1.0 (default) scaling 1-4 interactions (values used in AMBER: 2.0, 1.2, 1.0) c c c iscreen = 0 (default) atom independent screening length c = 1 atom dependent screening length c arithmetic mixing rule for screening lengths c sl=0.5*(screen(atom-i) + screen(atom-j)) c = 2 atom dependent screening length, c geometric mixing rule for screening lengths c sl=sqrt(screen(atom-i) * screen(atom-j)) c- - - - - - c c Available in the program polarizability models (parameters): c 1) Applequist, 2) Thole-Tinker-like, 3) Thole-exp, 4) Thole-linear, c The following polarizability models and appropriate combinations of c input parameters are available in the program: c for: Thole-Tinker: ipol=2, Thole-exp: ipol=3, Thole-linear: ipol=4, and: c a)1-2,1-3 excluded, 1-4 scaled by 1.2: n12=0,n13=0,n14=1, scee=1.2, iscreen=0 c b)1-2,1-3 excluded, 1-4 scaled by 2.0: n12=0,n13=0,n14=1, scee=2.0, iscreen=0 c c)1-2,1-3 excluded, 1-4 not scaled: n12=0,n13=0,n14=1, scee=1.0, iscreen=0 c d)1-2,1-3 included: n12=1,n13=1,n14=1, scee=1.0, iscreen=0 c e)1-2,1-3 excluded, 1-4 scaled by 1.2: n12=0,n13=0,n14=1, scee=1.2, iscreen=1 c For: Applequist model: ipol=1, and: c a)1-2,1-3 excluded, 1-4 scaled by 1.2: n12=0,n13=0,n14=1, scee=1.2, iscreen=0 c b)1-2,1-3 excluded, 1-4 scaled by 2.0: n12=0,n13=0,n14=1, scee=2.0, iscreen=0 c c)1-2,1-3 excluded, 1-4 not scaled: n12=0,n13=0,n14=1, scee=1.0, iscreen=0 c d)1-2,1-3 included: n12=1,n13=1,n14=1, scee=1.0, iscreen=0 c c For all other polarizabilities models (i.e. other combination of n12,n13,n14,scee,iscreen) c use input from external file ( -ip polarizabilities.dat). c c c c NOTE: ESP coordinates must always be in Bohrs c input polarizabilities in a.u. C C-------------------------------------------------------------------------- C C -3rd- wtmol .... relative weight for the molecule if c multiple molecule fit (1.0 otherwise) C C FORMAT(F10.5) C C-------------------------------------------------------------------------- c c -4th- subtitle for molecule c C-------------------------------------------------------------------------- C c -5th- CHARGE,IUNIQ ( THE NUMBER OF UNIQUE CENTERS for this molecule) c C FORMAT(2I5) C C-------------------------------------------------------------------------- C -6th- ONE CARD FOR EACH UNIQUE CENTER C C FORMAT(I5,i5,5x,2f10.5) C C Name, IVARY, polarizability, screen_length C C NAME = ATOMIC number C C IVARY = CONTROL OF CHARGE VARIATION OF THIS CENTER C = 0 CHARGE VARIED INDEPENDENTLY OF PREVIOUS CENTERS C = -n CHARGE FROZEN AT "INITIAL CHARGE" VALUE C = n CHARGE FITTED TOGETHER WITH CENTER n C polarizability = the polarizability value for this atom C (units = a.u. ) C see "ipol" input variable in section: -2nd- above C sl = individual atomic screening length of polarization C read only if iscreen n.e. 0 C C------------------------------------------------------------------------- C C -7th- intra molecule charge constraints... blank line if no constr C C FORMAT(I5,F10.5) C C ngrp = number of centers in the group associated with this C constraint (i.e. the number of centers to be read in) C C grpchg(i) = charge to which the associated group of atoms C (given on the next card) is to be constrained C C C -7.1- C imol,iatom (16I5) (repeat if more than 8 centers C C the list (ngrp long) of the atom indices of those atoms to be C constrained to the charge specified on the previous card. C c blank to end C C------------------------------------------------------------------------ c -8th- c intermolecular charge constraints (atoms must sum to the c specified value) c same format as indvidual molecule constraints c blank to end c C------------------------------------------------------------------------ c c -9th- c Multiple molecule constraints....constrain atoms on i to be c the same as on j c NGRP (I5) number of constaints C (imol,iatom) (16I5) (repeat card if more than 8 groups) c c blank to end c C------------------------------------------------------------------------ c c C Unit 3 (qin) input of replacement charges if requested c iqopt = 2,3 c c (8f10.6) (i = 1,iuniq) c c------------------------------------------------------------- c Unit 4 input if new weight factors if requested c c (i5) nqwt number of new weights to cycle thru c (f10.5) new weights (nqwt lines) c c-------------------------------------------------------------- C C Unit 10 input of ESP's (mandatory) C C natoms,nesp (i5,i6) C X , Y , Z . FORMAT (17X,3E16.7) C QUPOT , X , Y , Z . FORMAT (1X,4E16.7) C C QUPOT = THE QUANTUM MECHANICAL ELECTROSTATIC C POTENTIAL ( A.U ) C C X,Y,Z = THE COORDINATE AT WHICH THE POTENTIAL C IS CALCULATED ( A.U ) C C NOTE : THE PROGRAM G80UCSF WRITES IN THIS FORMAT BUT THE C OUTPUT OF G90 MUST BE TRANSLATED (PROGRAM BOHR). C C-------------------------------------------------------------- C C Unit 11 input of polarizabilities and screen_length types (only if ipol ne 0) C C Reading atomic polarizabilities from "-ip polarizabilities" file. C The file contains polarizabilities for each atom type used C in the program and screen_length(s). Individual, atom-dependent screening c lengths are read only if iscreen is not equal 0. c After reading polarizabilities (and screen_lengths) from unit 11 C program tries to assign them to the actual atoms for molecule(s). C Alternatively - the actual polarizabilities can be read from general C input, for each atom separately, see at record no.: -6th- above. C The actual polarizabilities override those that program eventually C tries to assign to atoms by itself. C The polarizabilities in the polariz file depend on the value of ipol C parameter (see line: -2nd- above). C C iattype(i),polarizability(i),screen_length(i) (a2,2f10.5) C C iattype - atom type C polarizability - the polarizability value c where i runs over polarizability types c screen_length = read when atom dependent screening length is used c for polarization charge fitting c c If screening length is atom-independent then read it after the input c of all polarizability types: c c a, screen_length (a2,f10.5) c c a - just a letter "a" c screen_length - additional parameter for Thole models c (necessary if iscreen = 0) c C C-------------------------------------------------------------- c c How to run the program: c c usage: i_resp -i input -o output -p punch -q qin -t qout \ c -e espot -w qwts -s esout -ip polarizabilities c c c if ipol.ne.0 the program produces in the first stage: the esp.qm-induced c file which is used in the second stage as input with option: c -e esp.qm-induced c C--------------------------------------------------------------