[gmx-users] Principal Component Analysis

[bharat gupta]

Hi,

I want to perform the dihedral PCA for two residues of a turn region in a
protein i.e 4 dihedral angles. I have created an index file for the atoms
constituting phi and psi angles for those two residues. But I don't
understand what has to be written in covar file .. According to manual it
says "covar.ndx, which necessarily contains one group of atom 1 to
integer(2*N/3), where N is the number of dihedral angles". This means that
covar should contain 1 2 3 (for 4 dihedrals). Here's teh steps that I
followed till now.

1. Make an index file for residues 116 , 117 phi-psi angles . Here's its
contents :
[phi-psi-116-117]
1797 1799 1801 1809
1799 1801 1809 1811
1809 1811 1813 1816
1811 1813 1816 1818
2. used _angle -f mdrun.xtc  -n index-dihedral.ndx -or dangle.trr -type
dihedral -b 5000 -e 10000
3. trjconv -s mdrun.tpr -f dangle.trr -o resiz.gro -n covar.ndx -e . Here's
the content for resiz.gro file :
Generated by trjconv : Protein in water t=   0.00000
    3
    1ALA      N    1  -0.234   0.972   0.083
    1ALA     H1    2   0.997  -0.944  -0.329
    1ALA     H2    3  -0.017  -1.000   0.000
   2.00000   2.00000   2.00000
Why there is alanine here in this file ??





Regards
----------------------
Bharat