From: Asma El-Magboub (elmagbou_at_usc.edu)
Date: Thu Jan 22 2015 - 21:32:09 CST
Hello Sir/Madam
I hope my email finds you well. I am using NAMD to study dynamic properties of a group of molecules, where all these molecules are structurally related: part of structures of these molecule should be completely planer, where it is a conjugated pi system. Topology and parameters data are generated using charmm force field (https://cgenff.paramchem.org/) that used to generate psf file and run namd. After minimization I noticed that my molecules were entirely lose their planarity, which make simulations' outcomes suboptimal. By reviewing the topology file I found that only 2 improper torsions have been assigned. So manually I added another 17 impropers to maintain the planarity of the conjugated system of my molecules. I used this new edited topology file to successfully generate solvated psf files. However, namd was unable to find improper parameters! is there any way to solve this problem.
Here there is the impropers list that I couldn't find there parameter info in order to proceed with namd simulations (note some of them are repeated more than one time):
"IMPROPERS
CG2DC1 CG2O5 CG2D1O HGA4
CG2DC1 CG2DC1 CG2O5 HGA4
CG2DC2 CG2D1O CG2DC2 HGA4
CG2DC1 CG2R61 CG2DC1 HGA4
CG2DC2 CG2DC2 CG2R61 HGA4
CG2R61 CG2R61 CG2DC1 CG2R61
CG2R61 CG2DC2 CG2R61 CG2R61
CG2R61 CG2R61 CG2R61 HGR61
CG2R61 CG2R61 CG2R61 OG301
CG2R61 CG2R61 CG2R61 OG311
CG2R61 CG2R61 CG2R61 HGR61"
Regards,
Asma S. El-Magboub
M.Sc. Pharmaceutical Sciences
PhD Student
Department of Pharmacology and Pharmaceutical Sciences
School of Pharmacy
University of Southern California
Los Angeles, CA 90089
Email: elmagbou_at_usc.edu / elmagboub_at_gmail.com
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