Hi,
On Fri, Feb 1, 2019 at 7:12 AM Shirin Jamshidi <shirinjamshidi.gmail.com> wrote:
>
> readdata evec.pev analyze modes fluct file evec.pev beg 1 end 1 out
> flucmode1
It looks like you've combined a 'readdata' command with a 'modes'
command. These need to be separate. I highly recommend reading the
manual entries for these commands so you understand what the commands
and their keywords do (for example, the 'file' keyword is deprecated -
cpptraj should be printing a message to this effect). You want
something like:
readdata evec.pev
modes fluct name evec.pev beg 2 end 2 out flucmode2
modes fluct name evec.pev beg 3 end 3 out flucmode3
...
runanalysis
Hope this helps,
-Dan
>
> readdata evec.pev analyze modes fluct file evec.pev beg 2 end 2 out
> flucmode2
>
> readdata evec.pev analyze modes fluct file evec.pev beg 3 end 3 out
> flucmode3
>
> readdata evec.pev analyze modes fluct file evec.pev beg 4 end 4 out
> flucmode4
>
> readdata evec.pev analyze modes fluct file evec.pev beg 5 end 5 out
> flucmode5
>
> readdata evec.pev analyze modes fluct file evec.pev beg 6 end 6 out
> flucmode6
>
> readdata evec.pev analyze modes fluct file evec.pev beg 7 end 7 out
> flucmode7
>
> readdata evec.pev analyze modes fluct file evec.pev beg 8 end 8 out
> flucmode8
>
> readdata evec.pev analyze modes fluct file evec.pev beg 9 end 9 out
> flucmode9
>
> readdata evec.pev analyze modes fluct file evec.pev beg 10 end 10 out
> flucmode10
>
>
>
> projection modes evec.pev out proj.ppj beg 1 end 9999.CA,N1
>
>
>
>
>
>
>
>
>
> *Error:*
>
> Error: reading datafile flucmode1
>
> Error: Could not read data file 'evec.pev'.
>
> 1 errors encountered reading input.
>
> Error: Error(s) occurred during execution.
>
>
>
> CPPTRAJ: Trajectory Analysis. V17.00
>
> ___ ___ ___ ___
>
> | \/ | \/ | \/ |
>
> _|_/\_|_/\_|_/\_|_
>
>
>
> | Date/time: 01/31/19 16:37:29
>
> | Available memory: 1.727 GB
>
>
>
> Reading '*.prmtop' as Amber Topology
>
> Radius Set: modified Bondi radii (mbondi)
>
> INPUT: Reading input from 'mode.in'
>
> [trajin *_md3.mdcrd]
>
> Reading '*N_md3.mdcrd' as Amber Trajectory
>
> Warning: *_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.
>
> [readdata evec.pev analyze modes fluct file evec.pev beg 1 end 1 out
> flucmode1]
>
> Reading 'evec.pev' as Evecs file with name 'evec.pev'
>
> Reading modes from evec.pev
>
> File contains 9273 modes.
>
> Reading modes from analyze
>
> Reading modes from modes
>
> Reading modes from fluct
>
> Reading modes from file
>
> Reading modes from evec.pev
>
> Warning: DataSet 'evec.pev' already present.
>
> Reading modes from beg
>
> Reading modes from 1
>
> Reading modes from end
>
> Reading modes from 1
>
> Reading modes from out
>
> Reading modes from flucmode1
>
> TIME: Total execution time: 32.3959 seconds.
>
> On Tue, Jan 22, 2019 at 11:01 AM Shirin Jamshidi <shirinjamshidi.gmail.com>
> wrote:
>
> >
> > Dear AMBER developers,
> >
> > I have a problem in second stage of running essential dynamics to obtain
> > the diverse top modes in AMBER 16. I used to apply the same codes and
> > script in previous versions of amber and there was no problem at all.
> > However, since I have installed AMBER16, I always get the below error when
> > I am going to run fluctmode script after obtaining evec.pev file.
> >
> > evec.pev file exists in my working directory and I have no idea how I
> > need to change my code to be compatible to run again as usual.
> >
> > I appreciate very much any help, guidance or thought from you.
> >
> > Best regards,
> > Shirin
> >
> >
> > *command:*
> > cpptraj *.prmtop -i mode.in > mode.out
> >
> > *mode.in <http://mode.in> script:*
> > trajin *.mdcrd
> >
> > rms first mass :1-3090.CA,N1
> >
> > analyze modes fluct file evec.pev beg 1 end 1 out flucmode1
> > analyze modes fluct file evec.pev beg 2 end 2 out flucmode2
> > analyze modes fluct file evec.pev beg 3 end 3 out flucmode3
> > analyze modes fluct file evec.pev beg 4 end 4 out flucmode4
> > analyze modes fluct file evec.pev beg 5 end 5 out flucmode5
> > analyze modes fluct file evec.pev beg 6 end 6 out flucmode6
> > analyze modes fluct file evec.pev beg 7 end 7 out flucmode7
> > analyze modes fluct file evec.pev beg 8 end 8 out flucmode8
> > analyze modes fluct file evec.pev beg 9 end 9 out flucmode9
> > analyze modes fluct file evec.pev beg 10 end 10 out flucmode10
> >
> > projection modes evec.pev out proj.ppj beg 1 end 47448 .CA,N1
> >
> > *Error:*
> > Error: 'evec.pev' not found: Modes should be read in prior to this command
> > with 'readdata'
> >
> > 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 Fri Feb 01 2019 - 05:30:03 PST
