Dear Amber users,
I am using the pH-REMD simulation with Amber, but I have some problems
connected with reconstruction of pH-based trajectory files.
*When I perform cpptraj command:*
cpptraj exp.modO.parm7 traj.in
*where traj.in <
http://traj.in> file is:*
trajin exp_remd_pH2_5_00001.nc.000 remdtraj remdtrajtemp 5.0
exp_remd_pH3_0_00001.nc.001, exp_remd_pH3_5_00001.nc.002,
exp_remd_pH4_0_00001.nc.003, exp_remd_pH4_5_00001.nc.004,
exp_remd_pH5_0_00001.nc.005, exp_remd_pH5_5_00001.nc.006,
exp_remd_pH6_0_00001.nc.007
trajout REMD_only_5pH_00001.nc
*I recieve the next error:*
"Reading 'exp.modO.parm7' as Amber Topology
Radius Set: H(N)-modified Bondi radii (mbondi2)
INPUT: Reading input from 'traj.in'
[trajin exp_remd_pH2_5_00001.nc.000 remdtraj remdtrajtemp 5.0
exp_remd_pH3_0_00001.nc.001,exp_remd_pH3_5_00001.nc.002,
exp_remd_pH4_0_00001.nc.003, exp_remd_pH4_5_00001.nc.004,
exp_remd_pH5_0_00001.nc.005, exp_remd_pH5_5_00001.nc.006,
exp_remd_pH6_0_00001.nc.007]
Found 1 replicas.
Reading 'exp_remd_pH2_5_00001.nc.000' as Amber NetCDF
Error: Some or all replicas are missing temperature info.
Error: Could not set up input trajectory 'exp_remd_pH2_5_00001.nc.000'.
1 errors encountered reading input.
TIME: Total execution time: 0.5414 seconds.
Error: Error(s) occurred during execution. "
Execution of the run is performed with pmemd.cuda.MPI, I use AMBER18 for
the pH-REMD running and AMBER16 for cpptraj.
I hope you can help me.
Thank you in advance!
Best regards,
Elvira.
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Received on Wed Nov 14 2018 - 20:30:03 PST
