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 Tue Jan 22 2019 - 03:30:02 PST
