VMD-L Mailing List

From: Tobias Mandrup Johansen (tmj_at_rex2000.dk)
Date: Thu Sep 19 2002 - 10:04:42 CDT

Hi,

we have been having a problem that one of you might be able to explain.

When running vmd-1.7.1 on HPUX 11 i get this error

vmd > mol load psf LE-H2O.psf
Info) REMARKS original generated structure x-plor psf file
Info) Atom:1 SN: ENK ID: 1 RN: TYR NM: N TP: NT Q=-0.300
M=+14.007
Info) Atom:2 SN: ENK ID: 1 RN: TYR NM: HT1 TP: HC Q=+0.350
M=+1.008
Info) Atom:3 SN: ENK ID: 1 RN: TYR NM: HT2 TP: HC Q=+0.350
M=+1.008
Info) Atom:4 SN: ENK ID: 1 RN: TYR NM: HT3 TP: HC Q=+0.350
M=+1.008
Info) Loading new molecule ...
Info) Analyzing structure ...
Info) Atoms: 12848
Info) Residues: 4262
Info) Waters: 4257

Warning) Unusual bond between residues 4 and 5
Info) Segments: 2
Info) Fragments: 4258 Protein: 1 Nucleic: 0
vmd > animate read dcd LE_md_3.dcd
Info) Opened coordinate file LE_md_3.dcd for reading.
Info) DCD file type: CHARMm
vmd > IOT trap (core dumped)

is there anyone that knows how to fix this?

thanks!
Tobias