[AMBER] Regarding output file processing of temperature replica exchange

From: Rajarshi Roy <phd1701171011.iiti.ac.in>
Date: Wed, 14 Nov 2018 17:31:50 +0530

Dear Amber users and developer team
I am running a REMD simulation. After the simulation when I am trying to
extract the trajectories with respect to temperature using *remdtraj*
and *remdtrajtemp
*then it is showing

*"Target replica not found. Check that all replica trajectoriesError:
were found and that the target temperature or indices are validError: for
this ensemble." *
I am not able to figure out how to solve this problem.

Here I am writing the sample output and I attached the complete output file
for your better understanding, I have some following questions regarding
the output also.
---------------------------------------------------------------------

CPPTRAJ: Trajectory Analysis. V16.00
    ___ ___ ___ ___
     | \/ | \/ | \/ |
    _|_/\_|_/\_|_/\_|_

| Date/time: 11/14/18 16:59:58
| Available memory: 76.178 GB

INPUT: Reading input from '300.in'
  [parm complex_solv.prmtop]
        Reading 'complex_solv.prmtop' as Amber Topology
  [trajin remd_glycanD.mdcrd.001 remdtraj remdtrajtemp 300.00]
        Found 72 replicas.
        Reading 'remd_glycanD.mdcrd.001' as Amber NetCDF
Warning: Box information present in topology but not in trajectory.
Warning: DISABLING BOX in topology 'complex_solv.prmtop'!
  [trajin remd_glycanD.mdcrd.002 remdtraj remdtrajtemp 300.00]
Warning: Replica# found lower than file specified with trajin.
Warning: Found "remd_glycanD.mdcrd.001"; 'trajin remdtraj' requires
lowest # replica.
        Found 71 replicas.
        Reading 'remd_glycanD.mdcrd.002' as Amber NetCDF
  [trajin remd_glycanD.mdcrd.003 remdtraj remdtrajtemp 300.00]
Warning: Replica# found lower than file specified with trajin.
Warning: Found "remd_glycanD.mdcrd.002"; 'trajin remdtraj' requires
lowest # replica.
        Found 70 replicas.
        Reading 'remd_glycanD.mdcrd.003' as Amber NetCDF
  [trajin remd_glycanD.mdcrd.004 remdtraj remdtrajtemp 300.00]
Warning: Replica# found lower than file specified with trajin.
Warning: Found "remd_glycanD.mdcrd.003"; 'trajin remdtraj' requires
lowest # replica.
        Found 69 replicas.
        Reading 'remd_glycanD.mdcrd.004' as Amber NetCDF
.....................
1. Why replica number is reducing in each step?
....
Target replica not found. Check that all replica trajectories
Error: were found and that the target temperature or indices are valid
Error: for this ensemble.
....
2. Why amber is asking for all the replica as I already upload all the
replicas?
I also attached my input file.
Please help me out from this problem. As I am new in the replica exchange
md simulation so it is very difficult for me to understanding the error and
debug it .
Thank you in advance!
-- 
*with regards*
*Rajarshi Roy*
*PhD Research Scholar*
*Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*India*




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Received on Wed Nov 14 2018 - 04:30:02 PST
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