I am using amber 16 on Ubuntu 14.04 LTS and attempting to follow the antechamber tutorial 4b.
http://ambermd.org/tutorials/basic/tutorial4b/ .
When I try to look at the crd file from the minimization step (min.in) using VMD (using the 1FKO_sus.prmtop file), it is unable to read the crd file. The error given is:
Using plugin crd for coordinates from file ...........Problem reading CRD file
When I try to create a pdb from the minimized structure using the command ambpdb -p 1FKO_sus.prmtop ....... in the tutorial, it fails with the error
Error: Could not read restart atoms/time.
I was able to generate a pdb file within tleap using savepdb complex 1FKO_sus.pdb and this pdb read into VMD OK but it goes wrong after that. The jobs took a sensible amount of time to run and the relevant files are there.
Any idea what could be wrong?
thanks,Andy.
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Received on Thu Aug 04 2016 - 15:00:03 PDT
