VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Wed Aug 28 2019 - 12:50:35 CDT

The selection text after '-sel' needs to be in quotation marks: "protein
backbone and resid 70 71 72 73 74", otherwise only the first word,
'protein' gets used.

On Wed, Aug 28, 2019 at 1:02 PM ridaka jannat <ridaka.jannat_at_gmail.com>
wrote:

> 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
>
>