Re: getting different dihedral energy with two identical backbones

From: Joyce Yang (
Date: Mon Sep 29 2014 - 21:15:54 CDT

Thanks for the suggestion!

I have VMD 1.9.2, beta, but when I used " backbone" in the selection
(autopsfgen tool), it still write pdb and psf for the entire protein,
should i use something different?

Also, is the pairinteractionself just not working for selected dihedrals or
it also include everything for calculating electrostatic and vdw as well?



On Fri, Sep 26, 2014 at 5:18 PM, Jim Phillips <> wrote:

> Hi Joyce,
> Looking at the code in Molecule.C I can see that pairInteractionSelf isn't
> going to behave as you expect for dihedrals etc. that contain both selected
> and non-selected atoms. This a bug and it is easily fixable.
> A workaround is that, since the latest VMD beta (at least) can write full
> psf files, you can load each structure into VMD, make a selection of the
> backbone atoms, and write those selected atoms out as psf and pdb files
> that you can then load into NAMD for energy evaluation.
> Jim
> On Wed, 24 Sep 2014, Joyce Yang wrote:
> Hi,
>> I used the pairinteractionself function to calculated energy of the
>> backbones of two structures (one is obtained from mutating a single
>> residue
>> with vmd plugin), respectively. The settings are as below,
>> "pairInteraction on
>> pairInteractionGroup1 1
>> pairInteractionFile namd-temp.pdb
>> pairInteractionSelf on
>> coordinates namd-temp.pdb
>> "
>> The beta-coupling column of backbone atoms are set to 1 in the pdb files.
>> Surprisingly, the calculated dihedral angle energy of the backbones are
>> different in over 100 kcal/mol between the two structures. It doesn't
>> really make any sense to me since the two backbones are identical
>> (RMSD=0).
>> Anyone has an explanation for this?
>> Thanks
>> Joyce yang
>> Department of Chemistry
>> University of Alabama at Birmingham
>> Email:

Hongyi Yang
Graduate Student of Chemistry
Department of Chemistry
University of Alabama at Birmingham
Knowledge that changes the world.

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