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interpol_traj.f95
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interpol_traj.f95
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program inputreader
IMPLICIT NONE
integer :: nfrs,n,nmol,natoms
CHARACTER(32) :: anly
open(unit=5,file="protname.txt",status='old')
read(5,*)
read(5,*)n
read(5,*)nfrs
READ(5,*)natoms
close(5)
nfrs=10 !Number of interpolated frames
WRITE(*,*)n,nfrs
call traj(n,nfrs,natoms)
STOP
End program inputreader
subroutine traj(n,nfrs,natoms)
IMPLICIT NONE
INTEGER :: n,nfrs,i,j,k,a,iatom,natoms,ncoords,resnum(n),atomnum(n),mode
DOUBLE PRECISION :: rx(n,nfrs),ry(n,nfrs),rz(n,nfrs),rxcom(nfrs),rycom(nfrs),rzcom(nfrs),x(natoms,nfrs),y(natoms,nfrs)
DOUBLE PRECISION :: rxavg(n),ryavg(n),rzavg(n),xim(3*n,nfrs),rdeg,degr,pi,z(natoms,nfrs)
DOUBLE PRECISION :: QINV(3*n,3*n),xix(3*n,nfrs),xiy(3*n,nfrs),xiz(3*n,nfrs),theta(3*n,nfrs),phi(3*n,nfrs)
CHARACTER(32) :: atom,res,protname,aa,bb
CHARACTER(164) :: line
CHARACTER(3),Dimension(n) :: resname
OPEN(unit=12,file='mode',status='old')
READ(12,*)mode
CLOSE(12)
WRITE(*,*)mode
rxavg=0.0
rxcom=0.0
ryavg=0.0
rycom=0.0
rzavg=0.0
rzcom=0.0
QINV=0.0
xix=0.0
xiy=0.0
xiz=0.0
xim=0.0
theta=0.0
phi=0.0
x=0.0
y=0.0
z=0.0
pi=3.141592653589
degr=((2.0*pi)/360.0) !deg to rad
rdeg=1.0/degr !rad to deg
OPEN(unit=12,file='3N_QHAINVmatrix.dat',status='old')
DO a=1,3*n
DO i=1,3*n
READ(12,*)QINV(a,i)
END DO
END DO
CLOSE(12)
OPEN(unit=12,file='com_avg_coor',status='old')
DO i=1,n
READ(12,*)rxavg(i),ryavg(i),rzavg(i)
END DO
CLOSE(12)
!Read in interpolated frames from PDB file
WRITE(aa,*)mode
aa=adjustl(aa)
OPEN(unit=13,file='min'//TRIM(aa)//'.pdb')
!OPEN(unit=13,file='test.pdb')
!WRITE(*,*)'interpol1.pdb'
!DO k=1,nfrs !Loop over conformations
k=1 !Read minimum
DO i=1,5 !Read through TRJCONV header
READ(13,*)
END DO
j=0
!WRITE(*,*)k
DO a=1,natoms !Loop over atoms
READ(13,'(A)')line
!WRITE(*,*)line
READ(line(14:16),'(A)')res
read(line(33:39),'(F8.3)')x(a,k)
read(line(41:47),'(F8.3)')y(a,k)
read(line(49:55),'(F8.3)')z(a,k)
IF (res .EQ. "CA")THEN !Select out the coordinates of the alpha-carbons
!WRITE(*,*)line
j=j+1
read(line(33:39),'(F8.3)')rx(j,k) !Adjust due to chain information
read(line(41:47),'(F8.3)')ry(j,k) !Adjust due to chain information
read(line(49:55),'(F8.3)')rz(j,k) !Adjust due to chain information
rx(j,k)=rx(j,k)/10.0 !Convert to nm
ry(j,k)=ry(j,k)/10.0 !Convert to nm
rz(j,k)=rz(j,k)/10.0 !Convert to nm
!WRITE(*,*)rx(j,k),ry(j,k),rz(j,k)
rxcom(k)=rxcom(k)+rx(j,k)
rycom(k)=rycom(k)+ry(j,k)
rzcom(k)=rzcom(k)+rz(j,k)
!rxavg(j)=rxavg(j)+rx(j,k)
!ryavg(j)=ryavg(j)+ry(j,k)
!rzavg(j)=rzavg(j)+rz(j,k)
read(line(24:26),'(i3)')resnum(j)
read(line(8:11),'(i4)')atomnum(j)
read(line(18:20),'(A)')resname(j)
END IF
END DO
!READ(13,*)
rxcom(k)=rxcom(k)/REAL(n)
rycom(k)=rycom(k)/REAL(n)
rzcom(k)=rzcom(k)/REAL(n)
DO j=1,n !Centre-of-mass coordinates
rx(j,k)=rx(j,k)-rxcom(k)-rxavg(j)
ry(j,k)=ry(j,k)-rycom(k)-ryavg(j)
rz(j,k)=rz(j,k)-rzcom(k)-rzavg(j)
!rxavg(j)=rxavg(j)+rx(j,k)
!ryavg(j)=ryavg(j)+ry(j,k)
!rzavg(j)=rzavg(j)+rz(j,k)
!WRITE(*,*)rx(j,k),ry(j,k),rz(j,k)
END DO
CLOSE(13)
OPEN(unit=13,file='max'//TRIM(aa)//'.pdb')
k=nfrs !Read maximum
DO i=1,5 !Read through TRJCONV header
READ(13,*)
END DO
j=0
!WRITE(*,*)k
DO a=1,natoms !Loop over atoms
READ(13,'(A)')line
!WRITE(*,*)line
READ(line(14:16),'(A)')res
read(line(33:39),'(F8.3)')x(a,k)
read(line(41:47),'(F8.3)')y(a,k)
read(line(49:55),'(F8.3)')z(a,k)
IF (res .EQ. "CA")THEN !Select out the coordinates of the alpha-carbons
!WRITE(*,*)line
j=j+1
read(line(33:39),'(F8.3)')rx(j,k) !Adjust due to chain information
read(line(41:47),'(F8.3)')ry(j,k) !Adjust due to chain information
read(line(49:55),'(F8.3)')rz(j,k) !Adjust due to chain information
rx(j,k)=rx(j,k)/10.0 !Convert to nm
ry(j,k)=ry(j,k)/10.0 !Convert to nm
rz(j,k)=rz(j,k)/10.0 !Convert to nm
!WRITE(*,*)rx(j,k),ry(j,k),rz(j,k)
rxcom(k)=rxcom(k)+rx(j,k)
rycom(k)=rycom(k)+ry(j,k)
rzcom(k)=rzcom(k)+rz(j,k)
!rxavg(j)=rxavg(j)+rx(j,k)
!ryavg(j)=ryavg(j)+ry(j,k)
!rzavg(j)=rzavg(j)+rz(j,k)
read(line(24:26),'(i3)')resnum(j)
read(line(8:11),'(i4)')atomnum(j)
read(line(18:20),'(A)')resname(j)
END IF
END DO
!READ(13,*)
rxcom(k)=rxcom(k)/REAL(n)
rycom(k)=rycom(k)/REAL(n)
rzcom(k)=rzcom(k)/REAL(n)
DO j=1,n !Centre-of-mass coordinates
rx(j,k)=rx(j,k)-rxcom(k)-rxavg(j)
ry(j,k)=ry(j,k)-rycom(k)-ryavg(j)
rz(j,k)=rz(j,k)-rzcom(k)-rzavg(j)
!rxavg(j)=rxavg(j)+rx(j,k)
!ryavg(j)=ryavg(j)+ry(j,k)
!rzavg(j)=rzavg(j)+rz(j,k)
!WRITE(*,*)rx(j,k),ry(j,k),rz(j,k)
END DO
CLOSE(13)
!Now interpolate between these frames
DO k=2,9
DO j=1,natoms
x(j,k)=x(j,1)+(k-1)*((x(j,nfrs)-x(j,1))/(nfrs-1))
y(j,k)=y(j,1)+(k-1)*((y(j,nfrs)-y(j,1))/(nfrs-1))
z(j,k)=z(j,1)+(k-1)*((z(j,nfrs)-z(j,1))/(nfrs-1))
END DO
END DO
!Write interpolated coordinates to file and find Ca
DO k=2,nfrs-1
WRITE(bb,*)k
bb=adjustl(bb)
OPEN(unit=13,file='min'//TRIM(aa)//'.pdb')
OPEN(unit=14,file='interpol_'//TRIM(aa)//'.pdb',position='append',status='unknown')
WRITE(14,'(A)')'MODEL '//TRIM(bb)
DO i=1,5
READ(13,*)
END DO
j=0
!WRITE(*,*)k
DO a=1,natoms !Loop over atoms
READ(13,'(A)')line
!WRITE(*,*)line
READ(line(14:16),'(A)')res
IF (res .EQ. "CA")THEN !Select out the coordinates of the alpha-carbons
!WRITE(*,*)line
j=j+1
read(line(33:39),'(F8.3)')rx(j,k)
read(line(41:47),'(F8.3)')ry(j,k)
read(line(49:55),'(F8.3)')rz(j,k)
rx(j,k)=rx(j,k)/10.0 !Convert to nm
ry(j,k)=ry(j,k)/10.0 !Convert to nm
rz(j,k)=rz(j,k)/10.0 !Convert to nm
rx(j,k)=x(a,k)/10.0
ry(j,k)=y(a,k)/10.0
rz(j,k)=z(a,k)/10.0
!WRITE(*,*)rx(j,k),ry(j,k),rz(j,k)
rxcom(k)=rxcom(k)+rx(j,k)
rycom(k)=rycom(k)+ry(j,k)
rzcom(k)=rzcom(k)+rz(j,k)
!rxavg(j)=rxavg(j)+rx(j,k)
!ryavg(j)=ryavg(j)+ry(j,k)
!rzavg(j)=rzavg(j)+rz(j,k)
read(line(24:26),'(i3)')resnum(j)
read(line(8:11),'(i4)')atomnum(j)
read(line(18:20),'(A)')resname(j)
WRITE(*,*)rx(j,k),ry(j,k),rz(j,k)
END IF
!Write the interpolated coordinates to file
write(line(32:38),'(F7.3)')x(a,k)
write(line(40:46),'(F7.3)')y(a,k)
write(line(48:54),'(F7.3)')z(a,k)
WRITE(14,'(A)')line
END DO
CLOSE(13)
rxcom(k)=rxcom(k)/REAL(n)
rycom(k)=rycom(k)/REAL(n)
rzcom(k)=rzcom(k)/REAL(n)
DO j=1,n !Centre-of-mass coordinates
rx(j,k)=rx(j,k)-rxcom(k)-rxavg(j)
ry(j,k)=ry(j,k)-rycom(k)-ryavg(j)
rz(j,k)=rz(j,k)-rzcom(k)-rzavg(j)
!rxavg(j)=rxavg(j)+rx(j,k)
!ryavg(j)=ryavg(j)+ry(j,k)
!rzavg(j)=rzavg(j)+rz(j,k)
!WRITE(*,*)rx(j,k),ry(j,k),rz(j,k)
END DO
WRITE(14,'(A)')'TER'
WRITE(14,'(A)')'ENDMDL'
END DO !End loop over interpolated frames
CLOSE(14)
DO k=1,nfrs
!Now calculate mode trajectories
a=mode
do j=1,3*n !residue loop
IF(MOD(j,3) .EQ. 1)xix(mode,k)=qinv(mode,j)*rx(j,k)+xix(mode,k)
IF(MOD(j,3) .EQ. 2)xiy(mode,k)=qinv(mode,j)*ry(j,k)+xiy(mode,k)
IF(MOD(j,3) .EQ. 0)xiz(mode,k)=qinv(mode,j)*rz(j,k)+xiz(mode,k)
end do
xim(a,k)=(xix(a,k)**2+xiy(a,k)**2+xiz(a,k)**2)**.5
! calculate theta, phi
theta(mode,k)=acos(xiz(mode,k)/xim(mode,k))
phi(mode,k)=atan(xiy(mode,k)/xix(mode,k))
if(xix(a,k).lt.0.0)phi(a,k)=phi(a,k)+pi
theta(a,k)=theta(a,k)*rdeg
if(phi(a,k).lt.0.0)phi(a,k)=phi(a,k)+2.0*pi
phi(a,k)=phi(a,k)*rdeg
WRITE(*,*)theta(a,k),phi(a,k)
WRITE(aa,*)mode
aa=adjustl(aa)
END DO
OPEN(unit=25,file='interpol'//TRIM(aa)//'_traj.dat',status='unknown')
DO k=1,nfrs
!WRITE(*,*)'Writing the trajectory for mode ',a
WRITE(25,*)theta(mode,k),phi(mode,k)
END DO
CLOSE(25)
end subroutine