VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Wed Aug 28 2019 - 13:18:08 CDT

Those are not errors. The plugin is simply letting you know there are no
nucleic acids for it to restrain (which is good, because your selection
text specifies 'protein').

On Wed, Aug 28, 2019 at 1:57 PM ridaka jannat <ridaka.jannat_at_gmail.com>
wrote:

> Thanks for your reply.
> I have used the quotation mark but now getting this following error
>
> ssrestraints) Restraining protein residues...
> ssrestraints) The given selection does not contain nucleic acid.
>
> Is the command line I am using to keep the hbonds intact for these
> particular residues, correct?
>
> On Wed, Aug 28, 2019 at 12:50 PM Ryan McGreevy <ryanmcgreevy_at_ks.uiuc.edu>
> wrote:
>
>> 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
>>>
>>>