Gmx anadock: problem of pdb reading

User discussions
1

GROMACS version:2019
GROMACS modification: No

Hello,

I am using gmx anadock to analize ligand ensemble obtained from Autodock DLG file. Regardless of the input pdb I always get the following error:

Found 0 pdb files

Segmentation fault: 11

I double checked the pdb - it looks correct and it has been correctly recognized by other gromacs programs. Finally, I reconverted it to using gmx trjconv, which did not solve the issue (the new pdb still does not work with gmx anadock).

Looking forward to hearing your ideas

2

Hi,
Recently gmx anadock tool was removed from GROMACS (see release note http://manual.gromacs.org/current/release-notes/2020/major/removed-functionality.html?highlight=gmx%20anadock).
Maybe you can directly contact the authors.
Best regards
Alessandra

3

hello Alessandra,
thank you very much for this info!
Actually I’ve already noticed that other people also had similar problem with this tool related to recognition of input pdb filles. Could you suggest me the contacts of the authors anyway, I was not able to find it in the description of the program (it still exist in gmx2019 by the way!)

4

I just found an another alternative to gmx anadock that suggest to use gmx cluster for the same purposes:


I’ve already tried gmx cluster with my pdb and it works fine! are there an aditional sollution to sort results of gmx cluster based on cluster’s energies ?