Dear Jason,
I tried what you suggest, but unfortunately I get this message error:
CPPTRAJ: Trajectory Analysis. V13.1
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
AmberParm Title: [default_name]
Radius Set: modified Bondi radii (mbondi)
INPUT: Reading Input from STDIN
[trajin remd.mdcrd.001 remdtraj remdtrajtemp 302.28]
Found 80 replicas.
[remd.mdcrd.001] contains 551 frames.
Warning: RemdTraj: Replica remd.mdcrd.002 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.003 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.008 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.011 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.015 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.016 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.017 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.022 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.025 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.030 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.031 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.032 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.033 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.037 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.039 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.040 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.042 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.045 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.046 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.047 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.049 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.050 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.051 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.052 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.053 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.054 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.055 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.056 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.057 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.058 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.059 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.060 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.061 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.062 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.063 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.064 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.065 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.066 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.067 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.068 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.069 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.070 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.071 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.072 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.073 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.074 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.075 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.076 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.077 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.078 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.079 frames (552) does not match
Warning: # frames in first replica (551).
Warning: RemdTraj: Replica remd.mdcrd.080 frames (552) does not match
Warning: # frames in first replica (551).
[trajin remd_r2.mdcrd.001 remdtraj remdtrajtemp 302.28]
Found 80 replicas.
Warning: remd_r2.mdcrd.001: Could not accurately predict # frames. This usually
indicates a corrupted trajectory. Will attempt to read 554 frames.
[remd_r2.mdcrd.001] contains 554 frames.
Error: RemdTraj: Replica remd_r2.mdcrd.001 does not have temperature info.
Error: trajin: Could not set up trajectory.
I don't know what is happening with my run after the first one, it is like the files are not recognized.
It is really strange, because with another system everything goes right. I used Replica exchange in two different system with the same input file but here I get this error.
I used as input file for the analysis this file:
#!/bin/bash
cpptraj AVP_open.prmtop <<EOF
trajin remd.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r2.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r3.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r4.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r5.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r6.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r7.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r8.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r9.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r10.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r11.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r12.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r13.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r14.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r15.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r16.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r17.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r18.mdcrd.001 remdtraj remdtrajtemp 302.28
trajin remd_r19.mdcrd.001 remdtraj remdtrajtemp 302.28
trajout remd_300K.mdcrd nobox
go
EOF
I am so confused,
Do you have any idea?
Thank you in advance,
Nawel
________________________________________
De : Mele N. [nm10g13.soton.ac.uk]
Envoyé : vendredi 4 juillet 2014 21:22
À : AMBER Mailing List
Objet : Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories
Thanks you very much for your help,
I will try it tomorrow and let you know if it work.
________________________________________
De : Jason Swails [jason.swails.gmail.com]
Envoyé : vendredi 4 juillet 2014 20:58
À : AMBER Mailing List
Objet : Re: [AMBER] ptraj: Could not find target 302.280000 in any of the replica trajectories
On Fri, Jul 4, 2014 at 12:23 PM, Mele N. <nm10g13.soton.ac.uk> wrote:
> Thanks a lot for your answer,
>
> Actually I have a number of run for each replica, so you mean that just by
> providing the lowest replica it will recognized even all the different run?
>
No. You need to provide the lowest replica number for _each_ run on a
separate trajin or ensemble line.
>
> By the way I used amber12 , does it change the way to analyse the
> temperature trajectories compare to Amber14?
>
No difference.
For example:
trajin run1.mdcrd.000
trajin run2.mdcrd.000
trajin run3.mdcrd.000
...
Assuming you named your files run1.mdcrd.000, run1.mdcrd.001,
run.mdcrd.002, ... etc for the first run and then changed "run1" to "run2"
for the second run, etc.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Jul 05 2014 - 03:00:02 PDT
