[AMBER] problem with cpptraj

From: Marko Sever <Marko.Sever.ki.si>
Date: Thu, 10 Sep 2020 12:57:49 +0000


I have a problem with cpptraj. I installed it locally on my computer via the conda AmberTools installation method, which is provided on the Amber website.

The cpptraj program seems to start fine, but when I try to load a trajectory after loading the parameters file (psf or pdb) it says that there is an error in the number of atoms in the parameter file and in the trajectory.

Error: # atoms in DCD file (93892) does not match # atoms in parm step5_assembly.psf (93854)
Error: Could not set up 'blabla.dcd' for reading.
Error: Could not set up input trajectory 'blabla.dcd'.

The same parameter file+trajectory works fine on a HPC install od amber-18-gcc, in addition it works fine with Charmm, Namd and VMD. So in reality there isn't a mismatch between the two.

On the HPC I like to use cpptraj very much, it is very fast and would like to use it also on my local computer.

So there must be something wrong with the install/configuration of cpptraj on my local computer.

I tried both the Ambertools version 20 and 19, same behaviour.

Can you help me?


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Received on Thu Sep 10 2020 - 06:00:02 PDT
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