Dear Dan,
Many thanks for your reply.
The error has gone, the file could be found now but it seems there is
another problem with the script to work properly since it couldn’t read the
evec file for this time.
Please see the below script and the error as follows.
Many thanks again for your time.
Best,
Shirin
*Script:*
trajin *.mdcrd
rms first mass :1-3090.CA,N1
readdata evec.pev analyze modes fluct file evec.pev beg 1 end 1 out
flucmode1
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 - 04:30:02 PST
