Dear Friends,
I would like to perform the dihedral angle calculation of particular residue over the period of simulation time. Could you please help me out in creating the ndx file using make_ndx command. I tried but ended up with the error stating "number of index elements not multiple of 4 these cannot be dihedral quadruplets".
Alternatively, you can also try gmx rama for phi/psi dihedral combinations
Firstly, calculate dihedrals for all the residues as a function of time
gmx rama -s md.tpr -f md.xtc -o dihedrals.xvg
As per need, flags -b (first frame), -e (last frame) can be added
eg. gmx rama -s md.tpr -f md.xtc -b 1000 -e 5000 -o dihedrals.xvg
Later extract the dihedrals of specific residue (eg. ASN-103)
grep ASN-103 dihedrals.xvg | awk '{print $1 " " $2'} > rama-ASN-103.xvg
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