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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- application/octet-stream attachment: input.in
Received on Wed Nov 14 2018 - 04:30:02 PST
