Hi,
On Tue, Jan 22, 2019 at 6:01 AM Shirin Jamshidi
<shirinjamshidi.gmail.com> wrote:
> *Error:*
> Error: 'evec.pev' not found: Modes should be read in prior to this command
> with 'readdata'
This is the key error message: you need to read 'evec.pev' in prior to
issuing it as a command. Normally I try to maintain backwards
compatibility at all costs, but in this case I changed the syntax
slightly in order to support improvements to the underlying data
set/data file framework (see postscript for more details). This error
message was supposed to let you know what needs to be done to fix
things but I should make it more descriptive.
All you need to do is add 'readdata evec.pev' prior to all of your
'analyze modes' commands and everything should work.
Hope this helps,
-Dan
PS - Previously, the way your script would work under the hood is that
ptraj/cpptraj would load the file each time an 'analyze modes' command
was given. In the new code each 'analyze modes' command will use the
single loaded file.
>
> Error: Could not setup analysis [modes]
> 1 errors encountered reading input.
> Error: Error(s) occurred during execution.
>
> [1]+ Exit 1 cpptraj ../../../MexBpaHmemPAN.prmtop -i
> mode.in > mode.out
>
>
> *mode.out:*
> CPPTRAJ: Trajectory Analysis. V17.00
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 01/22/19 10:46:56
> | Available memory: 465.523 MB
>
> Reading '../../../MexBpaHmemPAN.prmtop' as Amber Topology
> Radius Set: modified Bondi radii (mbondi)
> INPUT: Reading input from 'mode.in'
> [trajin ../../../MexBpaHmemPAN_md3.mdcrd]
> Reading '../../../MexBpaHmemPAN_md3.mdcrd' as Amber Trajectory
> Warning: MexBpaHmemPAN_md3.mdcrd: Could not accurately predict # frames.
> This usually
> Warning: indicates a corrupted trajectory or trajectory/topology
> Warning: mismatch. Will attempt to read 71547 frames.
> [rms first mass :1-3090.CA,N1]
> RMSD: (:1-3090.CA,N1), reference is first frame (:1-3090.CA,N1),
> mass-weighted.
> Best-fit RMSD will be calculated, coords will be rotated and
> translated.
> [analyze modes fluct file evec.pev beg 1 end 1 out flucmode1]
> Warning: The 'analyze' prefix is no longer necessary and may be soon
> deprecated.
> Warning: To add an analysis command the the queue, only the command name
> needs
> Warning: to be specified, e.g. 'modes <args>'.
> Warning: Argument 'file' is deprecated, use 'name <modes>' instead.
> TIME: Total execution time: 0.9652 seconds.
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Received on Thu Jan 24 2019 - 08:30:02 PST
