VMD-L Mailing List

From: Akash Banerjee (akashneon_at_gmail.com)
Date: Mon Jan 18 2021 - 16:31:20 CST

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