CHARMM Development Project Forums CHARMM Community Script Archive complex PDB input examples

* build catalytic complex of IRK from PDB coords
* file split for CHARMM import
* IRK == Insulin Receptor Kinase fragment; ANP changed to ATP
*

bomblev -1

! STD FILES 
open unit 1 read card name -
  /usr/local/charmm/c29b2/toppar/top_all27_prot_na.rtf
read rtf card unit 1
close unit 1
open unit 1 read card name -
  /usr/local/charmm/c29b2/toppar/par_all27_prot_na.prm
read param card unit 1
close unit 1

! ALTERNATE PDB INPUT METHOD; put B-factors in WMAIN
read univ
* modified pdb
*
pdb
segid 22 1
ires 23 4
w 61 6
end

! PROTEIN FRAGMENT, SEGID A; GET SEQU AND COORDS FROM FILE
open unit 3 read card name irk.pdb
read sequ pdb unit 3
rewind unit 3
gener A setup warn 
read coor univ unit 3 offset -980
close unit 3

! ATTEMPT TO PLACE ANY MISSING HEAVY ATOMS
ic purge
ic param
ic fill preserve
ic build
define test sele ( .not. type H* ) .and. ( .not. init ) show end

! REBUILD ALL H ATOM COORDS
coor init sele type H* end
hbuild sele type H* end
define test sele .not. init show end

! SUBSTRATE FRAGMENT, SEGID B; GET SEQU AND COORDS FROM FILE
open unit 3 read card name iri.pdb
read sequ pdb unit 3
rewind unit 3
gener B setup warn first ace last ct3
read coor univ unit 3 offset 296
close unit 3

! ATTEMPT TO PLACE ANY MISSING HEAVY ATOMS
ic purge
ic param
ic fill preserve
ic build
define test sele segid B .and. ( .not. type H* ) .and. ( .not. init ) show end

! REBUILD ALL H ATOM COORDS
coor init sele segid B .and. type H* end
hbuild sele segid B .and. type H* end
define test sele segid B .and. .not. init show end

! ATP 
read sequ atp 1
gener N setup warn first none last none
open unit 3 read card name iratp.pdb
read coor univ unit 3 offset 309 
close unit 3

! PLACE ANY MISSING HEAVY ATOMS; REBUILD ALL H ATOM COORDS
ic purge
ic param
ic fill preserve
ic build
define test sele segid N .and. ( .not. type H* ) .and. ( .not. init ) show end
coor init sele segid N .and. type H* end
hbuild sele segid N .and. type H* end
define test sele segid N .and. .not. init show end

! MG++ IONS
read sequ mg 2
gener M setup warn first none last none
open unit 3 read card name irmg.pdb
read coor univ unit 3 offset 310
close unit 3

! XTAL WATER
read sequ tip3 202
gener W noang nodihe
open unit 3 read card name irwat.pdb
read coor univ unit 3 offset 312
close unit 3
hbuild sele segid W .and. type H* end

energy

open unit 4 write card name irki.psf
write psf  card unit 4
* insulin receptor kinase w. peptide, atp, mg++, water
*

open unit 4 write card name irki.crd
write coor card unit 4
* insulin receptor kinase w. peptide, atp, mg++, water; e = ?ENER
*

stop

* pertussis toxin from PDB; must read each subunit separately
* one of two molecules from the asymmetric unit of 1PRT
*

! RTF AND PARAM FILES
open unit 2 read card name /v/rhea1/charmm/c27b3/toppar/top_all22_prot.inp
read rtf card unit 2
close unit 2

open unit 2 read card name /v/rhea1/charmm/c27b3/toppar/par_all22_prot.inp
read param card unit 2
close unit 2

! SETUP UNIV COORD READER TO READ PDB FORMAT, PUT B FACTOR IN WMAIN
read univ
* modified pdb setup
*
pdb
w 61 6
end

! SUBUNIT A HAS A TEN RESIDUE GAP (DISORDERED LOOP); READ AS 2 FILES
! USE SETUP OPTION OF GENERATE TO CREATE IC TABLE
open unit 10 read card name 1prt-a.pdb
read sequ pdb unit 10
gener A setup warn
rewind unit 10
open unit 11 read card name 1prt-a2.pdb
read sequ pdb unit 11
gener A2 setup warn
rewind unit 11
join A A2

! SUBUNITS B-F; READ RESIDUE SEQUENCE AND REWIND FILE
open unit 12 read card name 1prt-b.pdb
read sequ pdb unit 12
gener B setup warn
rewind unit 12

open unit 13 read card name 1prt-c.pdb
read sequ pdb unit 13
gener C setup warn
rewind unit 13

open unit 14 read card name 1prt-d.pdb
read sequ pdb unit 14
gener D setup warn
rewind unit 14

open unit 15 read card name 1prt-e.pdb
read sequ pdb unit 15
gener E setup warn
rewind unit 15

open unit 16 read card name 1prt-f.pdb
read sequ pdb unit 16
gener F setup warn
rewind unit 16

! CONVERT ISOLATED CYS TO DISULFIDE LINK
patch disu A  41 A 201 setup sort warn
patch disu B  23 B  87 setup sort warn
patch disu B 120 B 134 setup sort warn
patch disu B 192 B 199 setup sort warn
patch disu C  23 C  87 setup sort warn
patch disu C 120 C 134 setup sort warn
patch disu C 192 C 199 setup sort warn
patch disu D  31 D  51 setup sort warn
patch disu D 103 D 109 setup sort warn
patch disu E  31 E  51 setup sort warn
patch disu E 103 E 109 setup sort warn
patch disu F  27 F  41 setup sort warn
patch disu F  92 F  98 setup sort warn

! SAVE THE COMPLETED PSF
open unit 1 write card name pttox.psf
write psf card unit 1
* the six subunits (A-F) of pertussus toxin 1PRT; initial CHARMM psf
*

! OFFSETS REQUIRED TO PRESERVE PDB RESIDS
! OFFSET IS ADDED TO RESID TO GET CHARMM RESNO (ABSOLUTE RESIDUE NO.)
read coor univ unit 10 offset  -1
close unit 10
read coor univ unit 11 offset -11
close unit 11
read coor univ unit 12 offset 221
close unit 12
read coor univ unit 13 offset 417
close unit 13
read coor univ unit 14 offset 616
close unit 14
read coor univ unit 15 offset 726
close unit 15
read coor univ unit 16 offset 835
close unit 16

ic purge   ! CLEANUP IC TABLE
ic param   ! GET MISSING BONDS AND ANGLES FROM PARAMETER FILE
ic build   ! PLACE ANY MISSING COORDS, E.G. TERMINAL O ON CO2-

! CHECK FOR MISSING HEAVY ATOM COORDS
define test sele ( .not. type H* ) .and. ( .not. init ) show end

! SAVE THE IC TABLE FILLED WITH XTAL DATA
ic fill
open unit 1 write card name pttox.ic
write ic card unit 1
* the six subunits of pertussus toxin; initial CHARMM ic table
*
! USE HBUILD TO REBUILD H ATOMS; SPINS METHYLS, ETC. TO LOCAL MINIMUM
coor init sele type H* end
hbuild sele type H* end

! CHECK FOR ANY MISSING COORDS
define test sele .not. init show end

! SAVE THE COMPLETED CHARMM VERSION OF THE PDB XTAL COORDS
open unit 1 write card name pttox.crd
write coor card unit 1
* six subunits (A-F) of pertussus toxin 1PRT; initial CHARMM coords
*

stop