From: Gumbart, JC (
Date: Mon Feb 01 2021 - 09:49:35 CST

I think it should be possible to fit a single dihedral perfectly. Does the potential look unusual in some way?


On Jan 28, 2021, at 5:28 PM, Akash Banerjee <<>> wrote:

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,

On Mon, Jan 18, 2021 at 5:31 PM Akash Banerjee <<>> 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:*7C01*7Cgumbart**7C1fcaa9cfec7448969c2808d8c3e11e5f*7C482198bbae7b4b258b7a6d7f32faa083*7C0*7C0*7C637474718940642800*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000&sdata=cuzbs3vIOUSGSS3uZ*2BV*2BPJPHpZhrEmRT57cs9FshN*2F0*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!DZ3fjg!rosNPg98Dk_nDjXweqiovJnSTfWEhNVy3A6GHKef5se8fr9mpDK5lYggpXJ2-xIKWg$ >

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,