From: Arthur Pereira da Fonseca (
Date: Wed Sep 09 2020 - 12:16:46 CDT

Iím trying to run namdenergy on a dcd file.

This is the script:

set mol [mol new mypsf.psf type psf waitfor all]
mol addfile mydcd.dcd type dcd first 0 last -1 waitfor all molid $mol

set sell [atomselect top protein]

namdenergy -sel $sell -exe NAMD/namd2 -par par_all36_prot.prm -par par_all36_na.prm -par toppar_water_ions.str -all -tempname temp_file -ofile out_file

But Iím getting the follow error:

Info) Opened coordinate file temp_file_140000-temp.pdb for writing.
PDB WRITE ERROR: Position, occupancy, or b-factor (beta) for atom 53698
                 cannot be written in PDB format.
                 File will be truncated.
ERROR) write_timestep returned nonzero
Info) Finished with coordinate file temp_file_140000-temp.pdb.
atomsel: writepdb failed.

Iím gessing itís a problem with these atom coorddinates. Is it? How can i solve this problem?