remarks ++++++++++++++++PATCHTEST+++++++++++++++++++++++++++++ remarks Test case for the PATCH command remarks by Axel Brunger, JAN-1983 topology @CNS_TOPPAR:protein.top end parameter @CNS_TOPPAR:protein.param end topology PRESidue HISE ! Patch to change doubly protonated HIS to singly ! protonated histidine (HE2) ! has to be patched as REFErence=NIL= GROUP MODIFY ATOM CB TYPE CH2E CHARGE 0.0 END MODIFY ATOM CG TYPE C CHARGE 0.0 END GROUP MODIFY ATOM ND1 TYPE NR CHARGE -0.24 END MODIFY ATOM CE1 TYPE CR1E CHARGE 0.24 END GROUP MODIFY ATOM CD2 TYPE CR1E CHARGE 0.10 END MODIFY ATOM NE2 TYPE NH1 CHARGE -0.32 END MODIFY ATOM HE2 TYPE H CHARGE 0.22 END DELETE ATOM HD1 END ADD ACCEPTOR ND1 " " END {HISE} !-------------------------------------------------------------------------- PRES HISD ! Patch to change doubly protonated HIS to singly ! protonated histidine (HD1) ! has to be patched as REFErence=NIL= GROUP MODIFY ATOM CB TYPE CH2E CHARGE 0.00 END MODIFY ATOM CG TYPE C CHARGE 0.03 END GROUP MODIFY ATOM ND1 TYPE NH1 CHARGE -0.31 END MODIFY ATOM HD1 TYPE H CHARGE 0.22 END GROUP MODIFY ATOM CD2 TYPE CR1E CHARGE 0.09 END MODIFY ATOM NE2 TYPE NR CHARGE -0.25 END MODIFY ATOM CE1 TYPE CR1E CHARGE 0.22 END DELETE ATOM HE2 END ADD ACCEPTOR NE2 " " END {HISD} !----------------------------------------------------------------------- PRES HIST ! INVERSE PATCH TO HISD ! has to be patched as REFErence=NIL= GROUP MODIFY ATOM CB TYPE CH2E CHARGE 0.10 END MODIFY ATOM CG TYPE C CHARGE 0.15 END MODIFY ATOM CD2 TYPE CR1E CHARGE 0.20 END GROUP MODIFY ATOM ND1 TYPE NH1 CHARGE -0.25 END MODIFY ATOM HD1 TYPE H CHARGE 0.32 END GROUP MODIFY ATOM CE1 TYPE CR1E CHARGE 0.41 END GROUP MODIFY ATOM NE2 TYPE NH1 CHARGE -0.25 END ADD ATOM HE2 TYPE H CHARGE 0.32 END ADD BOND NE2 HE2 ADD ANGLE HE2 NE2 CD2 ADD ANGLE HE2 NE2 CE1 ADD IMPROPER NE2 CE1 CD2 HE2 ADD DONOR HE2 NE2 DELETE ACCEPTOR NE2 " " END {HISD} !--------------------------------------------------------------------- ! the following patch is somewhat strange: ! it shows what happens if one attempts to form groups between ! different residues in different segments PRESidue TES2 GROUP ADD ATOM 1XX TYPE C CHARGE 0.00 END ADD ATOM 1YY TYPE C CHARGE 0.00 END ADD ATOM 2YY TYPE C CHARGE 0.00 END MODIFY ATOM 2CA TYPE CH1E CHARGE 0.00 END DELETE BOND 1HT1 1N END {TES2} END !topology SEGMENT NAME=MAIN CHAIN @CNS_TOPPAR:protein.link SEQUENCE HIS HIS END END END SEGMENT NAME=COMP CHAIN @CNS_TOPPAR:protein.link SEQUENCE HIS HIS HIS HIS HIS END END END fix selection=( atom * * H* ) end patch hise refer=NIL=( atom comp 1 * ) end patch hisd refer=NIL=( atom comp 2 * ) end patch hist refer=NIL=( atom comp 2 * ) end delete selection=( atom comp 3 * OR atom comp 4 * OR atom comp 5 * ) end patch tes2 refer=1=( atom main 1 * ) refer=2=( atom comp 2 * ) end write structure end {* now test the handling of explicit exclusion lists during patch *} {* ============================================================== *} delete selection=( all ) end topology RESIDUE EX1 ATOM ABCD EXCLUSION=( B C ) END ATOM B EXCLUSION=( D ) END ATOM C END ATOM D END ATOM E END END RESIDUE EX2 ATOM A EXCLUSION=( B ) END ATOM B END END PRESIDUE EXP MODIFY ATOM 1ABCD EXCLUSION=( 1B 1C 1E 1X ) END MODIFY ATOM 2A EXCLUSION=( 1B 1ABCD 1X ) END ADD ATOM 1X EXCLUSION=( 2B ) END ADD BOND 1ABCD 2A END END SEGMENT NAME=TEST CHAIN SEQUENCE EX1 EX2 END END END WRITE STRUCTURE END PATCH EXP REFERENCE=1=( RESID 1 ) REFERENCE=2=( RESID 2 ) END WRITE STRUCTURE END struc reset end remarks Test multiple links. set echo=false end topology reset RESIdue ALA ATOM N TYPE=NH1 CHARge=-0.35 END ATOM H TYPE=H CHARge= 0.25 END ATOM CA TYPE=CH1A CHARge= 0.10 END ATOM CB TYPE=CH3E CHARge= 0.00 END ATOM C TYPE=C CHARge= 0.55 END !# ATOM O TYPE=O CHARge=-0.55 END !# BOND N CA BOND CA C BOND C O BOND N H BOND CA CB END {ALA} !------------------------------------------------------------------ RESIdue GLY ATOM N TYPE=NH1 CHARge=-0.35 END ATOM H TYPE=H CHARge= 0.25 END ATOM CA TYPE=CH1A CHARge= 0.10 END ATOM C TYPE=C CHARge= 0.55 END ATOM O TYPE=O CHARge=-0.55 END BOND N CA BOND CA C BOND C O BOND N H END {VAL} !--------------------------------------------------------------------- PRESidue L1 ADD DIHEDRAL -O -C +N +H ADD IMPRoper +N -C +CA +H {planar +N} END !--------------------------------------------------------------------- PRESidue L2 ADD DIHEDRAL -C +N +CA +C END !--------------------------------------------------------------------- PRESidue L3 ADD DIHEDRAL -N -CA -C +N ADD IMPRoper -C -CA +N -O {planar -C} END end set echo=true end segment name=" " chain link L1 head - ALA tail + * end link L2 head - * tail + ALA end link L3 head - * tail + * end ! sequence FOR GLY GLY ALA end coordinates ATOM 1 C ALA 1 9999.0009999.0009999.000 1.00 0.00 ATOM 2 O ALA 1 9999.0009999.0009999.000 1.00 0.00 ATOM 3 N GLY 2 9999.0009999.0009999.000 1.00 0.00 ATOM 4 H GLY 2 9999.0009999.0009999.000 1.00 0.00 ATOM 5 CA GLY 2 9999.0009999.0009999.000 1.00 0.00 ATOM 6 C GLY 2 9999.0009999.0009999.000 1.00 0.00 ATOM 7 O GLY 2 9999.0009999.0009999.000 1.00 0.00 ATOM 8 N GLY 3 9999.0009999.0009999.000 1.00 0.00 ATOM 9 H GLY 3 9999.0009999.0009999.000 1.00 0.00 ATOM 10 CA GLY 3 9999.0009999.0009999.000 1.00 0.00 ATOM 11 C GLY 3 9999.0009999.0009999.000 1.00 0.00 ATOM 12 O GLY 3 9999.0009999.0009999.000 1.00 0.00 ATOM 13 N ALA 4 9999.0009999.0009999.000 1.00 0.00 ATOM 14 H ALA 4 9999.0009999.0009999.000 1.00 0.00 ATOM 15 CA ALA 4 9999.0009999.0009999.000 1.00 0.00 ATOM 16 CB ALA 4 9999.0009999.0009999.000 1.00 0.00 ATOM 17 C ALA 4 9999.0009999.0009999.000 1.00 0.00 ATOM 18 O ALA 4 9999.0009999.0009999.000 1.00 0.00 END end end write structure end stop