rmsf-residue.str - CHARMM forums
2024年1月12日 · CHARMM variable R1 set to the (numerical!) resid of the first residue! NB: standard top_all22_na atom names are assumed for the backbone atoms!RESULT:! This file calculates nucleotide averaged RMS fluctuations! The average rmsf for the whole residue, backbone and sidechainis written to unit 21! N- and C-terminal atoms are included with the ...
CONS FIX and SHAP RESC - CHARMM forums
2006年1月4日 · CHARMM Development Project Forums User Discussion & Questions Energy terms, Constraints, Restraints, and Solvation CONS FIX and SHAP RESC: Forums Calendar Active Threads: Previous Thread: Next Thread : Print Thread: Page 1 of 2 : 1: 2: CONS FIX and SHAP RESC #9211 12/26/05 01:49 AM. Joined: Dec 2005. Posts: 13. B.
Energy terms, Constraints, Restraints, and Solvation - CHARMM …
2024年2月24日 · GBMV, ENER/ASP and INTE. by mywolfson. 02/08/08 04:55 PM
PDB to psf (basic question) - CHARMM forums
2006年4月24日 · Dear CHARMMers,I am trying to make a psf file from a pdb file with adding hydrogens, but I fail.The resulting pdb file changes drastically from the original one. I am afraid that this is too basic, but I appreciate your help. My input file …
CHARMM standard values for aromatic carbon
2024年2月18日 · Hi, among the two papers; "K. Vanommeslaeghe, 2012, ACS" and "K. Vanommeslaeghe, 2010, J Comput Chem" there is not a clear consensus about whether a carbon atom (not adjacent to a heteroatom) in an aromatic ring should always receive the value -0.115 - Is this the case ...
Measure distance between water and residue - CHARMM forums
2012年11月21日 · It is easy to check manually what the distance is in your file cell-final.crd. CHARMM can print the coordinate values for you (and you should check that they match what is in the file): print coor sele atom p1 66 OH .or. atom WAT 1761 OH2 end Now calculate the distance using those coordinates.
Relaxed potential energy scans - CHARMM forums
2004年4月16日 · I was thrilled when my optimized charmm surface fit the ab intio surface, but slightly less than thrilled when I found that the optimized structures differ by ninety degrees in the "optimized" torsion angle. Is my approach completely wrong or do I just have a subtle bug?
Carbopeptoid Parameters - CHARMM forums
2005年12月5日 · I am trying to run calculations on "Carbopeptoid Foldamers". As the monomers are not standard amino acids or standard sugars, should I be doing some sort of QM parameterisation in order to produce the monomer data for running in CHARMM.
Merge silicate with protein parameters - CHARMM forums
2011年1月30日 · CHARMM Development Project Forums User Discussion & Questions Parameter Set Discussion Merge silicate with protein parameters: Forums Calendar Active Threads: Previous Thread: Next Thread : Print Thread: Page 1 of 3 : 1: 2: 3: Merge silicate with protein parameters #26357 01/29/11 12:28 AM.
Does the free charmm version runs in parallel - CHARMM forums
I use free charmm and can run, but get very different results on one core and 4 cores. I use eef1 membrane model and Langevin dynamics, does anyone have some opinions on this kind of problem.