Hi,
The pH-REMD trajectory format changed in Amber 18, and cpptraj needed
to change in order to process it. So you need to use cpptraj from
Amber18 to process these trajectories. Let me know if you have trouble
with Amber 18 cpptraj doing this.
-Dan
On Wed, Nov 14, 2018 at 11:26 PM Elvira Tarasova
<elviratarasovachem.gmail.com> wrote:
>
> 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 Thu Nov 15 2018 - 05:30:03 PST
