Download Notes for using PROTPOL.f

Notes for Using PROTPOL.f
INPUT FILES:
UNIT = 5
protpol.d
line 1 TITLE
up to 80 characters
line 2 NPEP, NARO, NSUB, Ndis, NPRO
control variables
16A5
5I4
NPEP = no. of amide groups per subunit, generally one less than no. of residues
NARO = no. of aromatic (PHE+TYP+TRP) side chains
NSUB = no. of subunits (distinct from number of chains – all subunits must be
equivalent. i. e., have the same number of peptides, aromatics, disulfides,
Pro. A given subunit can consist of more than one chain and chains can
and do generally differ in number of peptides, etc.)
Ndis = no. of disulfide groups  10
NPRO = no. of Pro side chains  30
Ndis lines
NCys 1 (1), NCys 2 (1), NCys 1 (2). . .
18I4
(if Ndis ≠ 0)
NCys 1 (i) = no. or 1st residue in disulfide group i
NCys 2 (i) = no. of 2nd residue in disulfide group i
UNIT = 7
struct.pdb
protein coords.
line 1
line 2ff.
TITLE
up to 80 characters
16A5
ATYPE, RESTEST, NORES, (R(I,K),K=1,3)
13X,3A1,1X,A3,2X,I4,3F8.3
ATYPE = label identifying atom, e. g., N, CA, etc.
RESTEST = three-letter code for residue name
NORES = sequence number of residue
R(I,K) = x, y, z coordinates of atom, in Ǻ
Atomic coordinates in PDB format and in PDB order, i. e., N,CA, C, C, CB,…,.
Note that the coordinates are read, starting with the N of the N-terminal residue.
If there are multiple chains (i.e., gaps in the sequence), each chain must be
terminated with a line containing a blank at position 14. Files from the PDB
include this, starting with TER in positions 1-3, instead of ATOM.
OUTPUT FILES
UNIT = 6
protein.r
This file is used mainly for diagnostic purposes.
line 1
line 2
If Ndis ≠ 0
TITLE
title line from protein.d
NPEP, NARO, NSUB, Ndis, NPRO from protein.d
NCys 1 (1), NCys 2 (1), NCys 1 (2). . .
intermediate results
THETA = transition moment din. is Clark’s convention.
For each of the NPEP amide groups, four lines with ATYPE, RESTYPE, NORES,
((R(J,K), K = 1, 3), J = 1, 4)
ATYPE = type of atom (CA, C, O, N)
RESTYPE = name of residue contributing amino N
NORES = no. of residue contributing amino N
R = cartesian coords of atom
(note that the RESTYPE and NORES for the CA, C, O are incorrectly
given as those for the following residue – these parameters are only
correct for the N)
Followed by three lines with (Q(I, I), (H(J, I), J = 1, 3), I = 1, 3)
Q (I, I) = Ith diagonal element of moment of inertia matrix in principal
axis system, given in order of decreasing values
H(J, I) = unit vector in direction of IM principal axis, in protein coords.
These data are useful for detecting errors in reading coordinates. The principal
values for an amide should be near 3.0, 2.6 and 0.0. The third principal value is a
measure of deviation from a least-squares plane of the four atoms.
For each aromatic side chain, the diagonal elements of the moment of inertia and the
principal axes are given. For Phe, the diagonal elements should be ~ 5.7, 5.7, 0.0; for
Tyr 12.3, 5.8, 0.0; for Trp 21.7, 8.5, 0.0.
INDEX, NIDENT, NP,ISC-1
INDEX = total no. of transitions
NIDENT = total no. of non-zero one-electron matrix elements
NP = total no. of charge centers for static dipole moments
ISC-1=total no. of side-chain polarizable groups
4I5
A test is performed to determine whether the distance is ≤ 1.0 Å whenever a monopolemonopole interaction is calculated. If so, the following information is printed:
I, J, K, L, R1
4I6, F12.8
I = group 1 (transition or static charge density)
J = Monopole no. in group 1
K = group 2
L = monopole no. in group 2
R1 = distance (Å)
Now the V matrix is printed out. First, I is printed in format I4. This is the number of the
exciton level for which the matrix elements will be printed. Then for the upper half
of the V matrix, the matrix elements are printed, in cm-1.
V(I, J), J ≥ I.
6F12.5.
Then, for each exciton level:
WAVEL, ROTST
WAVEL = wavelength (nm)
ROTST = contribution of mixing with double excitations
The results are then printed. These consist of three lines per exciton level:
I, LAMBDA, DIP.STRENGTH, ROT.STR
I = no. of exciton level
LAMBDA = transition wavelength (nm)
DIP.STRENGTH = dipole strength (D2)
ROT.STRENGTH = rotational strength (DBM)
DIPOLE VELOCITY COMPONENTS
 x ,  y ,  z in Å-1
ANGULAR MOMENTUM COMPONENTS
(r x  )x, (r x  )y, (r x  )z in Bohr magnetons
These are followed by the eigenvector.
Sum rule tests:
ROTTOT = sum of rotational strength (should be small)
DIPTOT = sum of dipole strengths (should be ~ sum of monomer D
values)
For each exciton level, the changes in transition energy, summed over all polarizable
groups:
II, VK
II = no. of exciton level
VK = corrected transition frequency (cm-1)
For each exciton level, the corrections to dipole strength, summed over polarizable
groups
II, DIPST
II = no. of exciton level
DIPST = corrected dipole strength (D2)
For each exciton level:
V, TOTROT, DIPST, DELTA
V = wavelength (corrected) (nm)
TOTROT = total rotational strength (exciton + polarizable group contribn)
(DBM)
DIPST = corrected dipole strength (D2)
DELTA = band width (nm)
UNIT = 1
line 1
protein.o
TITLE
output file for calcg.CD, abs
from protein.d
Three sets of data with the results for each exciton transition
V, ROTST, DIPST, DELTA
V = wavelength of transition (nm)
ROTST = rotational strength (DBM)
DIPST = dipole strength (D2)
DELTA = band width (nm)
4F12.6
Delta is calculated as a weighted average of the band widths of the individual monomer
transitions. For the amide, these are 10.5 nm for the nπ*, 11.3 nm for NV1, 7.2 nm for
NV2. For aromatic and disulfide, see Sreerama’s website. The weighting factor is the
square of the coefficient for the basis transition in the eigenvector.
The first set has the results for the initial exciton calculation. The second set has the
exciton rotational strengths but the wavelengths and dipole strengths include the
polarizability contributions. The third set has the polarizability contributions to λ, R and
D.
UNIT = 10
Line 1
protein.t
eigenvector analysis
TITLE line: Contributions from individual transitions
THETA = 40 DEG
NV1 transition moment direction
Then a list of the basis functions:
function #
chromophore name and number
type of transition
Then for each exciton transition:
Molecular transition: (transition #) Wavelength: λ
followed by a listing of transitions that contribute 1% or more to the exciton
Notes for Using CDCALC.f
INPUT FILE:
UNIT = 5
cdcalc.dat
line 1 TITLE
up to 80 characters
line 2 NPEP, NARO, NSUB, Ndis, NPRO
input data
16A5
5I4
NPEP = no. of amide groups per subunit, generally one less than no. of residues
NARO = no. of aromatic (PHE+TYP+TRP) side chains
NSUB = no. of subunits (distinct from number of chains – all subunits must be
equivalent. i. e., have the same number of peptides, aromatics, disulfides,
Pro. A given subunit can consist of more than one chain and chains can
and do generally differ in number of peptides, etc.)
Ndis = no. of disulfide groups  10
NPRO = no. of Pro side chains  30
Ndis lines
NCys 1 (1), NCys 2 (1), NCys 1 (2). . .
18I4
(if Ndis ≠ 0)
NCys 1 (i) = no. or 1st residue in disulfide group i
NCys 2 (i) = no. of 2nd residue in disulfide group i
UNIT = 7
struct.pdb
protein coords.
line 1
line 2ff.
TITLE
up to 80 characters
16A5
ATYPE, RESTEST, NORES, (R(I,K),K=1,3)
13X,3A1,1X,A3,2X,I4,3F8.3
ATYPE = label identifying atom, e. g., N, CA, etc.
RESTEST = three-letter code for residue name
NORES = sequence number of residue
R(I,K) = x, y, z coordinates of atom, in Ǻ
Atomic coordinates in PDB format and in PDB order, i. e., N,CA, C, C, CB,…,.
Note that the coordinates are read, starting with the N of the N-terminal residue.
If there are multiple chains (i.e., gaps in the sequence), each chain must be
terminated with a line containing a blank at position 14. Files from the PDB
include this, starting with TER in positions 1-3, instead of ATOM.
OUTPUT FILES
UNIT = 6
protein.r
This file is used mainly for diagnostic purposes.
line 1
line 2
If Ndis ≠ 0
TITLE
title line from protein.d
NPEP, NARO, NSUB, Ndis, NPRO from protein.d
NCys 1 (1), NCys 2 (1), NCys 1 (2). . .
intermediate results