Hi there,
I want to calculate the overall rmsd (instead of backbone rmsd) between two proteins. I used a fortran code RMSD.f provided by you on web http://zhanglab.ccmb.med.umich.edu/TM-score/RMSD.f which is actually meant for calculating backbone RMSD. But, for overall RMSD, I made some changes in the code. Since I am new to fortran language, I am not very sure whether the result I am getting is correct or not.
I have only marked the below statement as comment, which I suppose was basically meant for chosing the C alpha.
ccccccccc read data from first CA file:
! if(s(13:16).eq.'CA '.or.s(13:16).eq.' CA '.or.s(13:16).
! & eq.' CA')then
! endif
ccccccccc read data from second CA file:
! if(s(13:16).eq.'CA '.or.s(13:16).eq.' CA '.or.s(13:16).
! & eq.' CA')then
! endif
Please suggest me whether the output obtained after this change is giving me the overall rmsd between two proteins.