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424 lines (341 loc) · 19.6 KB
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**** Warning **** The following extraneous characters
were found while command processing in CHARMM
2
CHARMM>
CHARMM> bomlev 0
CHARMM> prnlev 5
CHARMM> wrnlev 2
CHARMM>
CHARMM> if ?ensemble .ne. 1 then
RDCMND substituted energy or value "?ENSEMBLE" to "1"
Comparing "1" and "1".
IF test evaluated as false. Skip to ELSE or ENDIF
CHARMM>
CHARMM> set node ?whoiam
RDCMND substituted energy or value "?WHOIAM" to "1"
Parameter: NODE <- "1"
CHARMM> set setupdir /Users/williamglass/Documents/TMCS/Bristol/Project/AADH_EVB
Parameter: SETUPDIR <- "/USERS/WILLIAMGLASS/DOCUMENTS/TMCS/BRISTOL/PROJECT/AADH_EVB"
CHARMM> set setupdirOD1 /Users/williamglass/Documents/TMCS/Bristol/Project/AADH_EVB/charmm_evb_calcs/OD1
Parameter: SETUPDIROD1 <- "/USERS/WILLIAMGLASS/DOCUMENTS/TMCS/BRISTOL/PROJECT/AADH_EVB/CHARMM_EVB_CALCS/OD1"
CHARMM> set outputdir /Users/williamglass/Documents/TMCS/Bristol/Project/AADH_EVB/OD1_outputs
Parameter: OUTPUTDIR <- "/USERS/WILLIAMGLASS/DOCUMENTS/TMCS/BRISTOL/PROJECT/AADH_EVB/OD1_OUTPUTS"
CHARMM>
CHARMM> if @node .EQ. 0 set top state1
Parameter: NODE -> "1"
Comparing "1" and "0".
IF test evaluated as false. Skipping command
CHARMM> if @node .EQ. 1 set top state2
Parameter: NODE -> "1"
Comparing "1" and "1".
IF test evaluated as true. Performing command
Parameter: TOP <- "STATE2"
CHARMM>
CHARMM> !
CHARMM> ! READ IN TOPOLOGIES
CHARMM> !
CHARMM> ensemble open read unit 11 card name @setupdir/top_ttw@node.inp
Parameter: SETUPDIR -> "/USERS/WILLIAMGLASS/DOCUMENTS/TMCS/BRISTOL/PROJECT/AADH_EVB"
Parameter: NODE -> "1"
CHARMM> read rtf card unit 11
MAINIO> Residue topology file being read from unit 11.
TITLE> *>>>>>>>>CHARMM22 ALL-HYDROGEN TOPOLOGY FILE FOR PROTEINS <<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>>> AUGUST 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> *>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<<
TITLE> *>>>>>> 410-706-7442 OR EMAIL: ALEX,MMIRIS.AB.UMD.EDU <<<<<<<<<
TITLE> *
CHARMM> ensemble close unit 11
UNIT 11
CHARMM>
CHARMM> !
CHARMM> ! READ IN PARAMETERS
CHARMM> !
CHARMM>
CHARMM> ensemble open read form unit 1 name @setupdir/par_ttw.inp
Parameter: SETUPDIR -> "/USERS/WILLIAMGLASS/DOCUMENTS/TMCS/BRISTOL/PROJECT/AADH_EVB"
CHARMM> read parameter card unit 1
PARAMETER FILE BEING READ FROM UNIT 1
TITLE> *>>>> CHARMM22 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS <<<<<<<<<<
TITLE> *>>>>>>>>>>>>>>>>>>>>>> AUGUST 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
TITLE> *>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<<
TITLE> *>>>>>> 410-706-7442 OR EMAIL: ALEX,MMIRIS.AB.UMD.EDU <<<<<<<<<
TITLE> *
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
CHARMM> ensemble close unit 1
UNIT 1
CHARMM>
CHARMM> !
CHARMM> ! READ IN PSF & COOR
CHARMM> !
CHARMM> if @node .eq. 0 then
Parameter: NODE -> "1"
Comparing "1" and "0".
IF test evaluated as false. Skip to ELSE or ENDIF
CHARMM> if @node .eq. 1 then
Parameter: NODE -> "1"
Comparing "1" and "1".
IF test evaluated as true. Performing command
CHARMM> read psf card name @setupdirOD1/aadh_prod_od1_rename.psf
Parameter: SETUPDIROD1 -> "/USERS/WILLIAMGLASS/DOCUMENTS/TMCS/BRISTOL/PROJECT/AADH_EVB/CHARMM_EVB_CALCS/OD1"
VOPEN> Attempting to open::/USERS/WILLIAMGLASS/DOCUMENTS/TMCS/BRISTOL/PROJECT/AADH_EVB/CHARMM_EVB_CALCS/OD1/AADH_PROD_OD1_RENAME.PSF::
MAINIO> Protein structure file being read from unit 90.
TITLE> * QM/MM DYNAMICS WITH UMBRELLA SAMPLING
TITLE> * AADH: TRYPTAMINE NEW CRYSTAL STRUCTURE
TITLE> * 28/10/03
TITLE> * DATE: 4/ 1/16 12: 4:24 CREATED BY USER: kr8728
TITLE> *
PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
PSFSUM> Summary of the structure file counters :
Number of segments = 4 Number of residues = 1639
Number of atoms = 8179 Number of groups = 2608
Number of bonds = 8238 Number of angles = 8751
Number of dihedrals = 10799 Number of impropers = 696
Number of cross-terms = 0
Number of HB acceptors = 1772 Number of HB donors = 3173
Number of NB exclusions = 0 Total charge = -6.00000
VCLOSE: Closing unit 90 with status "KEEP"
CHARMM> endif
CHARMM>
CHARMM> read coor card name @setupdirOD1/path1_b3lyp_geom3.crd
Parameter: SETUPDIROD1 -> "/USERS/WILLIAMGLASS/DOCUMENTS/TMCS/BRISTOL/PROJECT/AADH_EVB/CHARMM_EVB_CALCS/OD1"
VOPEN> Attempting to open::/USERS/WILLIAMGLASS/DOCUMENTS/TMCS/BRISTOL/PROJECT/AADH_EVB/CHARMM_EVB_CALCS/OD1/PATH1_B3LYP_GEOM3.CRD::
SPATIAL COORDINATES BEING READ FROM UNIT 90
TITLE> * QM/MM DYNAMICS WITH UMBRELLA SAMPLING
TITLE> * AADH: TRYPTAMINE NEW CRYSTAL STRUCTURE
TITLE> * 28/10/03
TITLE> * DATE: 3/ 4/14 20:20:18 CREATED BY USER: KR8728
TITLE> *
** WARNING ** For atom in coordinate file, the corresponding residue in the PSF lacks that atom:
INDEX= 3030 IRES= 205 RESID=39 RES=TTW ATOM=HI2
** WARNING ** After reading, there are no coordinates for selected atom: 3331 224 ASP HI2
** A total of 1 selected atoms have no coordinates
*** LEVEL 2 WARNING *** BOMLEV IS 0
VCLOSE: Closing unit 90 with status "KEEP"
CHARMM> print coor card name @setupdirOD1/path1_b3lyp_geom3.crd
Parameter: SETUPDIROD1 -> "/USERS/WILLIAMGLASS/DOCUMENTS/TMCS/BRISTOL/PROJECT/AADH_EVB/CHARMM_EVB_CALCS/OD1"
COORDINATE FILE MODULE
TITLE> *
....
3321 224 ASP N 4.81900 -3.85800 -2.38000 BCHN 58 0.00000
3322 224 ASP HN 4.07800 -4.40100 -2.76600 BCHN 58 0.00000
3323 224 ASP CA 4.95100 -3.91200 -0.94600 BCHN 58 0.00000
3324 224 ASP HA 5.26000 -2.94200 -0.58100 BCHN 58 0.00000
3325 224 ASP CB 3.63900 -4.33600 -0.22700 BCHN 58 0.00000
3326 224 ASP HB1 3.29600 -5.30200 -0.61000 BCHN 58 0.00000
3327 224 ASP HB2 3.89200 -4.46800 0.83300 BCHN 58 0.00000
3328 224 ASP CG 2.49900 -3.29900 -0.29100 BCHN 58 0.00000
3329 224 ASP OD1 2.84200 -2.07700 -0.23000 BCHN 58 0.00000
3330 224 ASP OD2 1.32700 -3.75300 -0.32000 BCHN 58 0.00000
3331 224 ASP HI2 9999.000009999.000009999.00000 BCHN 58 0.00000
3332 224 ASP C 6.00200 -4.92800 -0.58700 BCHN 58 0.00000
3333 224 ASP O 6.08900 -5.99300 -1.19300 BCHN 58 0.00000
....
**** Warning **** The following extraneous characters
were found while command processing in CHARMM
NAME /USERS/WILLIAMGLASS/DOCUMENTS/TMCS/BRISTOL/PROJECT/AADH_EVB/CHARMM_EVB_CAL
CS/OD1/PATH1_B3LYP_GEOM3.CRD
CHARMM>
CHARMM> ! CALCULATE DIPOLE
CHARMM> !
CHARMM> ! This is needed to allow the calculation of state averaged dipole moments.
CHARMM> ! Useful in debugging/analysis. As there is only one molecule then we can use
CHARMM> ! 'sele all end'
CHARMM> !
CHARMM> ! coor dipo sele all end
CHARMM>
CHARMM> !
CHARMM> ! CALCULATE NON-EVB ENERGY
CHARMM> !
CHARMM> ! This is here for comparison with EVB energy calculation
CHARMM> !
CHARMM> energy
NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
There are 0 atom pairs and 0 atom exclusions.
There are 0 group pairs and 0 group exclusions.
<MAKINB> with mode 5 found 15633 exclusions and 10573 interactions(1-4)
<MAKGRP> found 3570 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 2350249 ATOM PAIRS AND 0 GROUP PAIRS
NBONDA>> Maximum group spatial extent (12A) exceeded.
Size is 10004.30 Angstroms and starts with atom: 3325
Please check group boundary definitions.
== PRIMARY == SPACE FOR 3525393 ATOM PAIRS AND 0 GROUP PAIRS
NBONDA>> Maximum group spatial extent (12A) exceeded.
Size is 10004.30 Angstroms and starts with atom: 3325
Please check group boundary definitions.
== PRIMARY == SPACE FOR 5288109 ATOM PAIRS AND 0 GROUP PAIRS
NBONDA>> Maximum group spatial extent (12A) exceeded.
Size is 10004.30 Angstroms and starts with atom: 3325
Please check group boundary definitions.
General atom nonbond list generation found:
3617241 ATOM PAIRS WERE FOUND FOR ATOM LIST
206708 GROUP PAIRS REQUIRED ATOM SEARCHES
ENER ENR: Eval# ENERgy Delta-E GRMS
ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ENER EXTERN: VDWaals ELEC HBONds ASP USER
---------- --------- --------- --------- --------- ---------
ENER> 0 0.16344E+12 0.00000E+00 0.17042E+06
ENER INTERN> 0.16344E+12 0.21416E+04 0.15674E+03 0.13786E+04 0.81477E+02
ENER EXTERN> 632.68694 -24225.10239 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
CHARMM>
CHARMM> !
CHARMM> ! SET UP EVB CALCULATION
CHARMM> !
CHARMM> ! Coupling parameters for 2-D Gaussian + a constant coupling
CHARMM> !
CHARMM> ! coupling of zero will give a EVB matrix with the energies of the states as the
CHARMM> ! eigenvalues.
CHARMM>
CHARMM> set CONS 0.0
Parameter: CONS <- "0.0"
CHARMM>
CHARMM> !
CHARMM> ! INITIALISE EVB CALCULATION
CHARMM> !
CHARMM> ! EVB hamiltonian matrix, H = :
CHARMM> !
CHARMM> ! state 1: |[0,0] [0,1]|
CHARMM> ! state 2: |[1,0] [1,1]|
CHARMM> !
CHARMM> ! Only modify upper triangular part as lower triangular part is filled in
CHARMM> ! automatically.
CHARMM> !
CHARMM> ! V0 and V1 and the potential energies of state 1 and 2 respectively.
CHARMM> !
CHARMM> ! EVBS : save unit for dipole output
CHARMM> ! SHFT 0 <VALUE> : H[0,0] <- V0 + <VALUE>
CHARMM> ! COUP 0 1 CONS <VALUE> : H[0,1] <- H[0,1] + <VALUE>
CHARMM> ! COUP 0 1 GAUS TWOD <2D GAUSSIAN> : H[0,1] <- H[0,1] + <2D GAUSSIAN>
CHARMM>
CHARMM> ensemble evb
Using Multi-Reference MM (EVB).
Ensemble EVB setting all 1 elements of the coupling matrix to a default value of zero.
Ensemble EVB setting all energy shifts to the default value of zero.
Energy will be the lowest eigenvalue of a 2 by 2 coupling matrix.
EVB> COUP 0 1 CONS @CONS
Parameter: CONS -> "0.0"
Reading terms for inclusion in EVB coupling element 0 - 1 ...
Specified term is a constant with value: 0.00000
EVB> envbi
ENVB...end of EVB input block
---------------------------------------------
Energy shift summary:
Node = 0 Shift = 0.00000
Node = 1 Shift = 0.00000
---------------------------------------------
---------------------------------------------
Coupling matrix element summary:
> Element which couples nodes 0 & 1 is a sum of the following terms:
>> Constant : 0.00000
---------------------------------------------
CHARMM>
CHARMM> energy
NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SHIFt VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
There are 3617241 atom pairs and 26206 atom exclusions.
There are 0 group pairs and 3570 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 5288109 ATOM PAIRS AND 0 GROUP PAIRS
NBONDA>> Maximum group spatial extent (12A) exceeded.
Size is 10004.30 Angstroms and starts with atom: 3325
Please check group boundary definitions.
General atom nonbond list generation found:
3617241 ATOM PAIRS WERE FOUND FOR ATOM LIST
206708 GROUP PAIRS REQUIRED ATOM SEARCHES
ENER ENR: Eval# ENERgy Delta-E GRMS
ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ENER EXTERN: VDWaals ELEC HBONds ASP USER
---------- --------- --------- --------- --------- ---------
ENER> 0 -0.17717E+05 0.16344E+12 0.16053E+02
ENER INTERN> 0.16344E+12 0.21416E+04 0.15674E+03 0.13786E+04 0.81477E+02
ENER EXTERN> 632.68694 -24225.10239 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
CHARMM>
CHARMM> !
CHARMM> ! RUN RELAXED SCAN
CHARMM> !
CHARMM> !ensemble open write card unit 21 name @outputdir/reaction.energy.@node
CHARMM>
CHARMM> !set atom1 BCHN 1 OD1
CHARMM> !set atom2 BCHN 1 HD1 ! think that this refers to the Asp residue in the BCHN
CHARMM> !set atom3 BCHN 1 OD2
CHARMM>
CHARMM> !set inc 0.1
CHARMM> !set v -1.0
CHARMM> !set n 1
CHARMM>
CHARMM> !label loop
CHARMM> ! skip none
CHARMM>
CHARMM> ! resd reset kval 2000.0 rval @v -
CHARMM> ! 1.0 @atom1 @atom2 -1.0 @atom2 @atom3
CHARMM>
CHARMM> ! mini abnr nstep 200 nprint 100
CHARMM>
CHARMM> ! skip resd
CHARMM> ! energy
CHARMM> ! write title unit 21
CHARMM> ! * @v ?ener
CHARMM> ! *
CHARMM>
CHARMM> !incr v by @inc
CHARMM> !incr n by 1
CHARMM> !if n .le. 21 goto loop
CHARMM>
CHARMM> !ensemble close unit 21
CHARMM>
CHARMM> stop
$$$$$$ New timer profile Local node$$$$$
List time 0.48 Other: 0.00
Electrostatic & VDW 0.20 Other: 0.00
Nonbond force 0.20 Other: 0.00
Bond energy 0.00 Other: 0.00
Angle energy 0.00 Other: 0.00
Dihedral energy 0.00 Other: 0.00
Restraints energy 0.00 Other: 0.00
INTRNL energy 0.01 Other: 0.00
Comm energy 0.00 Other: 0.00
Comm force 0.00 Other: 0.00
EVB MPI Comms 0.01 Other: 0.00
EVB Energy 0.00 Other: 0.00
EVB Forces 0.00 Other: 0.00
EVB routine 0.01 Other: 0.00
Energy time 0.21 Other: 0.00
Total time 1.20 Other: 0.51
$$$$$$ Average profile $$$$$
List time 0.48 Other: 0.00
Electrostatic & VDW 0.20 Other: 0.00
Nonbond force 0.20 Other: 0.00
Bond energy 0.00 Other: 0.00
Angle energy 0.00 Other: 0.00
Dihedral energy 0.00 Other: 0.00
Restraints energy 0.00 Other: 0.00
INTRNL energy 0.01 Other: 0.00
Comm energy 0.00 Other: 0.00
Comm force 0.00 Other: 0.00
EVB MPI Comms 0.01 Other: 0.00
EVB Energy 0.00 Other: 0.00
EVB Forces 0.00 Other: 0.00
EVB routine 0.01 Other: 0.00
Energy time 0.21 Other: 0.00
Total time 1.20 Other: 0.51
NORMAL TERMINATION BY NORMAL STOP
MOST SEVERE WARNING WAS AT LEVEL 2
$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 1.21 SECONDS
CPU TIME: 0.83 SECONDS
~
~
~