From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Wed Sep 09 2020 - 13:40:17 CDT

Hi Arthur,

Oof. You've probably got a coordinate greater than 9999 or less than -999.
How big is your system? If the system stays small enough, you could use
pbctools to rewrap everything so that the coordinates stay sane, or if it
is a centering problem, you would recenter with something like:

for { set f 0 } { $f < [molinfo top get numframes] } { incr f } {
$sell frame $f
$sell moveby [vecscale -1 [measure center $sell]]
}

-Josh

On Wed, Sep 9, 2020 at 11:42 AM Arthur Pereira da Fonseca <
arthurpfonseca3k_at_hotmail.com> wrote:

> Hello,
>
> I’m 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 I’m 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.
>
>
>
> I’m gessing it’s a problem with these atom coorddinates. Is it? How can i
> solve this problem?
>
>
>
> Thanks,
>
> Arthur
>