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From: ridaka jannat (ridaka.jannat_at_gmail.com)
Date: Wed Aug 28 2019 - 12:56:51 CDT

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
>>
>>