VMD-L Mailing List

From: Akash Banerjee (akashneon_at_gmail.com)
Date: Thu Jan 28 2021 - 16:28:57 CST

Hi VMD Developers,

I just wanted to follow up on the above ticket. Should I provide my input
files to clarify the issue? Please let me know if I could provide any
additional information that could help in this regard.

Thank you.

Kind regards,
Akash

On Mon, Jan 18, 2021 at 5:31 PM Akash Banerjee <akashneon_at_gmail.com> wrote:

> Hi FFTK/VMD developers,
>
> I am trying to resolve a dihedral in a polymer chain. I have generated the
> QM target data, but I am facing difficulties in fitting the dihedral to the
> target. I have enlisted my protocol below. Please have a look and advise me
> on how I could correct it.
>
> 1. Generated an optimized trajectory (fit to QM data), and used the
> modified PDB file for further studies.
> 2. Scanned the dihedral of interest (my molecule has several dihedrals). I
> only scan the one that is associated with a high penalty factor (assigned
> by CGenFF). I followed the routine given in the tutorial, i.e generated a
> QM input file for a negative (-180 to 0) and a positive (0 to 180) scan. I
> kept an interval of 5 degrees for both scans for better results.
> 3. The QM simulations were run on a remote resource, and QM log files were
> successfully generated.
> 3. In the optimize dihedrals tab, I uploaded the modified PDB , PSF, PAR
> and 2 QM target log files. I selected the dihedral that requires
> optimization, and I clicked the "run optimization" button. The resultant
> RMSD is 3.54.
> 4. I do refinements by adding dihedrals with different periodicity and
> phase shift angles. I referred to table 19 in this link:
> https://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield.pdf
>
> After trying several combinations (i.e all possible periodicity, phase
> shift angles, optimization algorithms and tolerance values), I get a RMSD
> of 2.2. I am not able to reduce the RMSD beyond the 2.2 mark.
>
> Do you have any insights into how I could get lower RMSD values, in turn
> improving the dihedral fitting protocol?
>
> Thank you.
>
> Kind Regards,
> Akash
>
>
> 

-- 
akash