Mahya Hemmat

3 Questions 2 Answers 0 Followers

Questions related from Mahya Hemmat

Parametrizing paclitaxol with CHARMM force field for molecular dynamics?

Hi, I'm trying to parametrize paclitaxol with CHARMM general forcefield 36 but I get the error " 4-membered ether ring not known. " Also, parametrizing the ligand with swissparm is not a good idea...

15 November 2017 8,767 3 View

Error: Constraint failure in RATTLE algorithm for atom 5380! in NAMD?

I'm trying to do SMD via NAMD, pulling one protein dimer away from another dimer. However, when I fix some of the atoms of the static dimer, and try to pull the other dimer away with constant...

06 July 2015 3,732 2 View

Can anyone help with this PSFgen error with VMD?

I'm trying to use the automatic PSFgen with VMD (via the software) and when I try to guess and split chains I get these errors: (for every pdb I try) >Unable to open file...

29 June 2015 550 4 View