Dear Guenter,
Acedrg has stopped producing the final output files of pdb format since
CCD/PDB introduced 5-letter ligand code, because pdb format could not
handle with that. However, it seems there are still strong requests for
the output pdb files, acedrg will produce pdb files when the ligand
codes are 3 letters or no ligand codes are input, in the coming new
version.
What I talked here is about running acedrg via command lines. I do not
know what happens in gui.
Best wishes,
Fei
On 2024-11-13 18:41, Guenter Fritz wrote:
Dear all,
I have a strange acedrg error. I usually run via command line for a
set of smiles.
If I run it from command line, the job runs, but acedrg writes only a
cif and not a pdb anymore.
If I run acedrg from the gui (ccp4i old gui) I get for any input
(smiles or cif) an error:
......
***************************************************************************
The program run with command:
/opt/software/CCP4/9.0/ccp4-9/bin/ccp4-python -m acedrg -c
/scratch/guenter/S100A9/glycine.cif -o
/home/guenter/PROJEKTE/NQR/152/152_14
has failed with error message
[19:31:32] non-ring atom 3 marked aromatic
***************************************************************************
#CCP4I TERMINATION STATUS 0 "[19:31:32] non-ring atom 3 marked
aromatic"
#CCP4I TERMINATION TIME 13 Nov 2024 19:31:35
#CCP4I MESSAGE Task failed
Any input is appreciated.
Thanks and best regards, Guenter
-------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
---
Dr. Fei Long
Structural Studies Division
UKRI Laboratory of Molecular Biology
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge
CB2 0QH UK
Email:fl...@mrc-lmb.cam.ac.uk
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
