VMD-L Mailing List

From: Marc Zimmer (mzim_at_conncoll.edu)
Date: Sat Sep 25 2010 - 06:26:24 CDT

Hi,

We have a 50ns MD trajectory from a Desmond simulation that we have loaded
on vmd and now want to do implicit ligand sampling to find the oxygen
pathways in our protein. When we try and do the implicit ligand sampling we
get the following error message, which we think might be due to or desmond
trajectory using different atom types that are not compatible with the
CHARMM parameter file.

Any suggestion would be appreciated

Paola and Ramza

*Could not assign VDW parameters to all atoms. Make sure you load the same
parameterfiles used for the MD simulation.

Warning) Could not find parameters for atom type HH22
Warning) Could not find parameters for atom type HN1
Warning) Could not find parameters for atom type HOH
Warning) Could not find parameters for atom type HXT
Warning) Could not find parameters for atom type HZ
Warning) Could not find parameters for atom type HZ1
Warning) Could not find parameters for atom type HZ2
Warning) Could not find parameters for atom type HZ3
Warning) Could not find parameters for atom type N
Warning) Could not find parameters for atom type N1
Warning) Could not find parameters for atom type N2
Warning) Could not find parameters for atom type N3
Warning) Could not find parameters for atom type NA
Warning) Could not find parameters for atom type ND1
Warning) Could not find parameters for atom type ND2
Warning) Could not find parameters for atom type NE
Warning) Could not find parameters for atom type NE2
Warning) Could not find parameters for atom type NH1
Warning) Could not find parameters for atom type NH2
Warning) Could not find parameters for atom type NZ
Warning) Could not find parameters for atom type O3
Warning) Could not find parameters for atom type OD1
Warning) Could not find parameters for atom type OD2
Warning) Could not find parameters for atom type OE1
Warning) Could not find parameters for atom type OE2
Warning) Could not find parameters for atom type OG
Warning) Could not find parameters for atom type OG1
Warning) Could not find parameters for atom type SD
Warning) Could not find parameters for atom type SG*