provide support for the RCSB PDBx/mmCIF file format

Author: jayponder

README.md

@@ -16,4 +16,4 @@ Tinker is the major release of the Ponder Lab tool set for molecular mechanics a
 
 Tinker is provided as a complete source distribution. After unpacking the release, you can build a set of Tinker executables on almost any machine with GNU gfortran or another modern Fortran compiler. Makefiles, a cmake configure script, as well as standalone scripts to compile, build object libraries, and link executables on a wide variety of machine-CPU-operating system combinations are provided. To build using the Tinker Makefile, just copy /make/Makefile into the /source area of the distribution. Small changes are needed near the top of the Makefile to set directory names and activate the appropriate operating system and compiler. Then issue the "make" command while in the /source directory.
 
-Note the FFTW libraries must be available prior to building Tinker. Pre-built FFTW libraries for some operating system and compiler combinations are provided under the /lib subdirectory of the source distribution. Or the libraries can be built following instructions in /fftw/0README.
+Note the FFTW libraries must be available prior to building Tinker. Pre-built FFTW libraries for some operating system and compiler combinations are provided under the /lib subdirectory of the source distribution. Alternatively, the libraries can be built following instructions in /fftw/0README.

cmake/CMakeLists.txt

@@ -105,57 +105,58 @@ set(_FILES
     chgpot chgtrn chkpole chkring chksymm chkxyz cholesky chrono chunks
     clock cluster column command connect connolly control couple cspline
     ctrpot cutoffs damping dcflux deflate delete deriv dexpol diagq diffeq
-    dipole disgeo disp dma domega dsppot eangang eangang1 eangang2 eangang3
-    eangle eangle1 eangle2 eangle3 eangtor eangtor1 eangtor2 eangtor3
-    ebond ebond1 ebond2 ebond3 ebuck ebuck1 ebuck2 ebuck3 echarge echarge1
-    echarge2 echarge3 echgdpl echgdpl1 echgdpl2 echgdpl3 echgtrn echgtrn1
-    echgtrn2 echgtrn3 edipole edipole1 edipole2 edipole3 edisp edisp1
-    edisp2 edisp3 egauss egauss1 egauss2 egauss3 egeom egeom1 egeom2 egeom3
-    ehal ehal1 ehal2 ehal3 eimprop eimprop1 eimprop2 eimprop3 eimptor
-    eimptor1 eimptor2 eimptor3 elj elj1 elj2 elj3 embed emetal emetal1
-    emetal2 emetal3 emm3hb emm3hb1 emm3hb2 emm3hb3 empole empole1 empole2
-    empole3 energi energy eopbend eopbend1 eopbend2 eopbend3 eopdist
-    eopdist1 eopdist2 eopdist3 epitors epitors1 epitors2 epitors3 epolar
-    epolar1 epolar2 epolar3 erepel erepel1 erepel2 erepel3 erf erxnfld
-    erxnfld1 erxnfld2 erxnfld3 esolv esolv1 esolv2 esolv3 estrbnd
-    estrbnd1 estrbnd2 estrbnd3 estrtor estrtor1 estrtor2 estrtor3 etors
-    etors1 etors2 etors3 etortor etortor1 etortor2 etortor3 eurey eurey1
-    eurey2 eurey3 evcorr ewald exfield expol extfld extra extra1 extra2
-    extra3 faces fatal fft fft3d fftpack field fields files final findnuc
-    findpro findseq flatten fracs freeunit freeze geometry getarc getcart
-    getdcd getint getkey getmol getmol2 getnumb getpdb getprm getref
-    getstring gettext getword getxyz ghmcstep gkstuf gradient gradrgd
-    gradrot group groups grpline gyrate hescut hessian hessn hessrgd
-    hessrot hpmf hybrid ielscf image impose improp imptor induce inertia
-    inform initatom initial initneck initprm initres initrot insert inter
-    invbeta invert iounit jacobi kanang kangang kangle kangs kangtor
-    kantor katom katoms kbond kbonds kcflux kcharge kchgflx kchgtrn kchrge
-    kcpen kctrn kdipol kdipole kdisp kdsp kewald kexpl kexpol kextra keys
-    kgeom khbond kimprop kimptor kinetic kiprop kitors kmetal kmpole
-    kmulti kopbend kopbnd kopdist kopdst korbit korbs kpitor kpitors
-    kpolar kpolpr kpolr krepel krepl ksolut ksolv kstbnd kstrbnd kstrtor
-    ksttor ktors ktorsn ktortor ktrtor kundrot kurey kurybr kvdw kvdwpr
-    kvdws lattice lbfgs light lights limits linmin lusolve makeint makeref
-    makexyz math maxwell mdinit mdrest mdsave mdstat mdstuf mechanic
-    merck merge minima molcul moldyn molecule moment moments mplpot mpole
-    mrecip mutant mutate nblist neck neigh nextarg nexttext nonpol nose
-    nspline nucleo number numeral numgrad ocvm omega opbend opdist openend
-    openmp optinit optsave orbital orbits orient orthog output overlap
-    params paths pbstuf pdb phipsi picalc piorbs pistuf pitors pme
-    pmestuf pmpb polar polgrp polopt polpcg polpot poltcg polymer potent
-    potfit predict pressure prmkey promo prtarc prtdyn prterr prtfrc
-    prtint prtmol2 prtpdb prtprm prtseq prtuind prtvel prtxyz ptable
-    qmstuf qrsolve quatfit random rattle readcart readdcd readdyn
-    readgau readgdma readint readmbis readmol readmol2 readpdb readprm
-    readseq readxyz refer repel replica reppot resdue respa restrn rgddyn
-    rgdstep richmond rigid ring rings rmsfit rotbnd rotlist rotpole
-    rxnfld rxnpot scales sdstep search sequen server setprm shakeup
-    shapes shunt sigmoid simplex sizes sktstuf socket solpot solute sort
-    square stodyn strbnd strtor suffix surface surfatom switch syntrn
-    tarray tcgstuf temper tettor tettors titles tncg torphase torpot
-    torque tors torsions tortor tree trimtext tritor tritors unionball
-    unitcell units uprior urey urypot usage valfit vdw vdwpot verlet
-    version vibs virial volume warp xtals xyzatm zatom zclose zcoord
+    dipole disgeo disp dma domega dsppot eangang eangang1 eangang2
+    eangang3 eangle eangle1 eangle2 eangle3 eangtor eangtor1 eangtor2
+    eangtor3 ebond ebond1 ebond2 ebond3 ebuck ebuck1 ebuck2 ebuck3 echarge
+    echarge1 echarge2 echarge3 echgdpl echgdpl1 echgdpl2 echgdpl3 echgtrn
+    echgtrn1 echgtrn2 echgtrn3 edipole edipole1 edipole2 edipole3 edisp
+    edisp1 edisp2 edisp3 egauss egauss1 egauss2 egauss3 egeom egeom1 
+    egeom2 egeom3 ehal ehal1 ehal2 ehal3 eimprop eimprop1 eimprop2
+    eimprop3 eimptor eimptor1 eimptor2 eimptor3 elj elj1 elj2 elj3 embed
+    emetal emetal1 emetal2 emetal3 emm3hb emm3hb1 emm3hb2 emm3hb3 empole
+    empole1 empole2 empole3 energi energy eopbend eopbend1 eopbend2
+    eopbend3 eopdist eopdist1 eopdist2 eopdist3 epitors epitors1 epitors2
+    epitors3 epolar epolar1 epolar2 epolar3 erepel erepel1 erepel2
+    erepel3 erf erxnfld erxnfld1 erxnfld2 erxnfld3 esolv esolv1 esolv2
+    esolv3 estrbnd estrbnd1 estrbnd2 estrbnd3 estrtor estrtor1 estrtor2
+    estrtor3 etors etors1 etors2 etors3 etortor etortor1 etortor2
+    etortor3 eurey eurey1 eurey2 eurey3 evcorr ewald exfield expol extfld
+    extra extra1 extra2 extra3 faces fatal fft fft3d fftpack field fields
+    files final findnuc findpro findseq flatten fracs freeunit freeze
+    geometry getarc getcart getdcd getfloat getint getkey getmol getmol2
+    getnumb getpdb getprm getref getstring gettext getword getxyz
+    ghmcstep gkstuf gradient gradrgd gradrot group groups grpline gyrate
+    hescut hessian hessn hessrgd hessrot hpmf hybrid ielscf image impose
+    improp imptor induce inertia inform initatom initial initneck initprm
+    initres initrot insert inter invbeta invert iounit jacobi kanang
+    kangang kangle kangs kangtor kantor katom katoms kbond kbonds kcflux
+    kcharge kchgflx kchgtrn kchrge kcpen kctrn kdipol kdipole kdisp kdsp
+    kewald kexpl kexpol kextra keys kgeom khbond kimprop kimptor kinetic
+    kiprop kitors kmetal kmpole kmulti kopbend kopbnd kopdist kopdst
+    korbit korbs kpitor kpitors kpolar kpolpr kpolr krepel krepl ksolut
+    ksolv kstbnd kstrbnd kstrtor ksttor ktors ktorsn ktortor ktrtor
+    kundrot kurey kurybr kvdw kvdwpr kvdws lattice lbfgs light lights
+    limits linmin lusolve makeint makeref makexyz math maxwell mdinit
+    mdrest mdsave mdstat mdstuf mechanic merck merge minima molcul moldyn
+    molecule moment moments mplpot mpole mrecip mutant mutate nblist neck
+    neigh nextarg nexttext nonpol nose nspline nucleo number numeral
+    numgrad ocvm omega opbend opdist openend openmp optinit optsave
+    orbital orbits orient orthog output overlap params paths pbstuf pdb
+    phipsi picalc piorbs pistuf pitors pme pmestuf pmpb polar polgrp
+    polopt polpcg polpot poltcg polymer potent potfit predict pressure
+    prmkey promo prtarc prtcif prtdyn prterr prtfrc prtint prtmol2 prtpdb
+    prtprm prtseq prtuind prtvel prtxyz ptable qmstuf qrsolve quatfit
+    random rattle readcart readcif readdcd readdyn readgau readgdma
+    readint readmbis readmol readmol2 readpdb readprm readseq readxyz
+    refer repel replica reppot resdue respa restrn rgddyn rgdstep richmond
+    rigid ring rings rmsfit rotbnd rotlist rotpole rxnfld rxnpot scales
+    sdstep search sequen server setprm shakeup shapes shunt sigmoid
+    simplex sizes sktstuf socket solpot solute sort square stodyn strbnd
+    strtor suffix surface surfatom switch syntrn tarray tcgstuf temper
+    tettor tettors titles tncg torphase torpot torque tors torsions tortor
+    tree trimtext tritor tritors unionball unitcell units uprior urey
+    urypot usage valfit vdw vdwpot verlet version vibs virial volume warp
+    xtals xyzatm zatom zclose zcoord
 )
 
 set(_LIB "")

doc/tinker-guide.pdf

@@ -1,2 +1,2 @@
-parameters    ../params/charmm36
+parameters    ../params/charmm36m
 verbose