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Commiting cleaned original copy of Q from csb to
leave it as an undeveloped old version branch following the same branching as django uses, that is, finished branches are created with: git branch stable/versionnumber and left there but not merged ever into master.
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‎.gitignore‎

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‎documentation/manuals/Qman5.tex‎

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@@ -12,6 +12,7 @@
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\usepackage{tabularx} %fixar långa tabeller
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\usepackage{multirow} %fixar nested tables
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\usepackage{bigstrut}
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\usepackage{bibentry}
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\newcommand{\dirfig}{./pictures}
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%\usepackage{hyperref}
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%\usepackage[linkbordercolor=1 1 1]{hyperref}
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\huge{PACKAGE} \Huge{Q}\\
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\vspace{0.7cm}
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\large{version 5.0\\
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January 1, 2004}\\
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\large{version 5.06\\
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June 27, 2007}\\
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\large{Q web site: http://xray.bmc.uu.se/aqwww/Q}
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\end{center}
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@@ -4264,6 +4265,15 @@ \subsubsection{Building the programs from source code}
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$\sim$/.cshrc).
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\end{enumerate}
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\section{HOW TO CITE}
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For citing this program please use the following citation:
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Marelius, J., Kolmodin, K., Feierberg, I. and Åqvist, J. Q: An MD
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program for free energy calculations and empirical valence bond
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simulations in biomolecular systems, J. Mol. Graphics Mod. 1999,
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16, 213-225.
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\newpage
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\begin{thebibliography}{2}

‎documentation/manuals/qman5.pdf‎

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‎src/Makefile.ake‎

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‎src/README‎

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In some machines path to intel fortran (ifort) compiler:
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For csh:
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Path to ifort compiler:
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source /home/apps/intel/bin/ifortvars.csh intel64
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setenv OMPI_FC ifort
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For bash:
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source /home/apps/intel/bin/ifortvars.sh intel64
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export OMPI_FC ifort
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This the same code as glenn with modification on el_scale and qq interactions
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setenv OMPI_FC ifort

‎src/avetr.f90‎

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@@ -1,90 +1,90 @@
1-
! (C) 2004 Uppsala Molekylmekaniska HB, Uppsala, Sweden
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!average co-ordinates from Qdyn trajectory files and write pdb-structure
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!Added to Qprep March 2004 by Martin Nervall
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!Tested to reproduce average structures from vmd
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module AVETR
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use PREP
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implicit none
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integer, parameter :: AVE_PDB = 11
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integer(4), private :: ncoords, N_sets = 0
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real(4), allocatable, private :: x_in(:), x_sum(:), x2_sum(:)
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real(8), private :: rmsd
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contains
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!TODO: *choose which frames, add more trajectories, divide x_sum every 100 steps
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!******************************************************
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!Main subroutine
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!******************************************************
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subroutine avetr_calc
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integer :: i, allocation_status
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character(len=1) :: ans
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logical :: fin
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N_sets = 0
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call trajectory
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ncoords = trj_get_ncoords()
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allocate(x_in(ncoords), x_sum(ncoords), x2_sum(ncoords), &
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stat=allocation_status)
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if (allocation_status .ne. 0) then
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write(*,*) 'Out of memory!'
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return
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end if
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do while(trj_read_masked(x_in)) !add from first file
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call add_coordinates
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end do
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!add from multiple files
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fin = .false.
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do while(.not. fin)
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CALL get_string_arg(ans, '-----> Add more frames? (y or n): ')
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if (ans .eq. 'y') then
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call trajectory
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do while(trj_read_masked(x_in)) !add from additional files
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call add_coordinates
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end do
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else
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fin = .true.
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end if
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end do
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call average
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call write_average
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deallocate(x_in, x_sum, x2_sum, stat=allocation_status)
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end subroutine avetr_calc
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!******************************************************
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!Sum the coordinates and the sqared coordinates
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!******************************************************
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subroutine add_coordinates
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x_sum = x_sum + x_in
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x2_sum = x2_sum + x_in**2
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N_sets = N_sets +1
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end subroutine add_coordinates
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!******************************************************
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!Make average and rmsd
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!******************************************************
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subroutine average
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x_sum = x_sum / N_sets
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x2_sum = x2_sum / N_sets
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rmsd = sqrt(sum(x2_sum - x_sum**2)/ncoords)
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end subroutine average
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!******************************************************
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!Write average coords to pdb file.
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!Variables used from prep: mask
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!Variables used from topo: xtop
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!******************************************************
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subroutine write_average
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!assign masked coordinates to right atom in topology
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call mask_put(mask, xtop, x_sum)
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call writepdb
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write(*,'(a,f6.3,a)') 'Root mean square co-ordinate deviation ', rmsd, ' A'
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x_sum = 0
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x2_sum = 0
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end subroutine write_average
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end module AVETR
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! (C) 2004 Uppsala Molekylmekaniska HB, Uppsala, Sweden
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!average co-ordinates from Qdyn trajectory files and write pdb-structure
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!Added to Qprep March 2004 by Martin Nervall
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!Tested to reproduce average structures from vmd
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module AVETR
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use PREP
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implicit none
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integer, parameter :: AVE_PDB = 11
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integer(4), private :: ncoords, N_sets = 0
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real(4), allocatable, private :: x_in(:), x_sum(:), x2_sum(:)
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real(8), private :: rmsd
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contains
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!TODO: *choose which frames, add more trajectories, divide x_sum every 100 steps
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!******************************************************
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!Main subroutine
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!******************************************************
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subroutine avetr_calc
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integer :: i, allocation_status
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character(len=1) :: ans
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logical :: fin
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N_sets = 0
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call trajectory
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ncoords = trj_get_ncoords()
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allocate(x_in(ncoords), x_sum(ncoords), x2_sum(ncoords), &
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stat=allocation_status)
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if (allocation_status .ne. 0) then
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write(*,*) 'Out of memory!'
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return
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end if
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do while(trj_read_masked(x_in)) !add from first file
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call add_coordinates
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end do
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!add from multiple files
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fin = .false.
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do while(fin == .false.)
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CALL get_string_arg(ans, '-----> Add more frames? (y or n): ')
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if (ans .eq. 'y') then
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call trajectory
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do while(trj_read_masked(x_in)) !add from additional files
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call add_coordinates
46+
end do
47+
else
48+
fin = .true.
49+
end if
50+
end do
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call average
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call write_average
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deallocate(x_in, x_sum, x2_sum, stat=allocation_status)
56+
end subroutine avetr_calc
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58+
!******************************************************
59+
!Sum the coordinates and the sqared coordinates
60+
!******************************************************
61+
subroutine add_coordinates
62+
x_sum = x_sum + x_in
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x2_sum = x2_sum + x_in**2
64+
N_sets = N_sets +1
65+
end subroutine add_coordinates
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67+
!******************************************************
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!Make average and rmsd
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!******************************************************
70+
subroutine average
71+
x_sum = x_sum / N_sets
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x2_sum = x2_sum / N_sets
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rmsd = sqrt(sum(x2_sum - x_sum**2)/ncoords)
74+
end subroutine average
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!******************************************************
77+
!Write average coords to pdb file.
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!Variables used from prep: mask
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!Variables used from topo: xtop
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!******************************************************
81+
subroutine write_average
82+
!assign masked coordinates to right atom in topology
83+
call mask_put(mask, xtop, x_sum)
84+
call writepdb
85+
write(*,'(a,f6.3,a)') 'Root mean square co-ordinate deviation ', rmsd, ' A'
86+
x_sum = 0
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x2_sum = 0
88+
end subroutine write_average
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90+
end module AVETR

‎src/calc_chemscore.f90‎

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@@ -165,7 +165,7 @@ module CALC_CHEMSCORE
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integer, private :: bDoTopcalc ! boolean flag
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integer, private :: iRestartCalc=-1 ! flag to indicate if doing calcs on restart file or not
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168-
logical, private :: bUseXIN = .false. ! boolean flag to indicate use of xin instead of xtop
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integer, private :: bUseXIN = 0 ! boolean flag to indicate use of xin instead of xtop
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integer, private :: warn ! flag to indicate if any warnings were displayed
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integer :: a,b,c !parameters
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real ::ab_sq,bc_sq,ca_sq, scp !local variables
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real, parameter :: pi = 4.0*atan(1.0)
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ab_sq = distsq(a,b)
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bc_sq = distsq(b,c)
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ca_sq = distsq(c,a)
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if ( scp > 1.0 ) scp = 1.0
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if ( scp < -1.0 ) scp = -1.0
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angle = acos(scp)*180.0/pi
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angle = acosd(scp)
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end function angle
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real function dist (a,b)
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end subroutine score_calc
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end module CALC_CHEMSCORE
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end module CALC_CHEMSCORE

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