VMD-L Mailing List

From: ridaka jannat (ridaka.jannat_at_gmail.com)
Date: Wed Aug 28 2019 - 12:01:28 CDT

Hello,

I was trying to use ssrestraints on the protein backbone and resid 70 to 74
to keep the hbonds intact for these particular residues to generate the
extrabonds file in namd.

I was using following command line

ssrestraints -psf XXX.psf -pdb XXX.pdb -o output2.dat -sel protein backbone
and resid 70 71 72 73 74 -hbonds

But I am getting following warnings

ssrestraints) Restraining protein residues...
ssrestraints) Warning: Phi dihedral angle of protein residue 0 will not be
restrained due to missing previous C atom.
ssrestraints: Warning: Psi dihedral angle of protein residue 1127 will not
be restrained due to missing next N atom.
ssrestraints) Warning: Phi dihedral angle of protein residue 1128 will not
be restrained due to missing previous C atom.
ssrestraints: Warning: Psi dihedral angle of protein residue 1315 will not
be restrained due to missing next N atom.
ssrestraints) Warning: Phi dihedral angle of protein residue 1316 will not
be restrained due to missing previous C atom.
ssrestraints: Warning: Psi dihedral angle of protein residue 1503 will not
be restrained due to missing next N atom.
.........
........
ssrestraints) The given selection does not contain nucleic acid.

Would you please help me with the script for restraing hbonds of some
residues? Is my command correct? Why I am getting this warnings?

Thank you