Dear Dan,
Thank you for your response!
Cpptraj works in Amber18, and it gives me the next output:
"
*Reading 'exp.modO.parm7' as Amber Topology Radius Set:
H(N)-modified Bondi radii (mbondi2)INPUT: Reading input from 'traj.in
<
http://traj.in>' [trajin exp_remd_pH2_5_00001.nc.000 remdtraj
remdtrajtemp 5.0 trajnames
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]
Reading 'exp_remd_pH2_5_00001.nc.000' as Amber NetCDFWarning: New
style (Amber >= V18) remd values detected with < 2 dimensions.Warning:
Assuming temperature.Warning: New style (Amber >= V18) remd values
detected with < 2 dimensions.Warning: Assuming temperature.Warning: New
style (Amber >= V18) remd values detected with < 2 dimensions.Warning:
Assuming temperature.Warning: New style (Amber >= V18) remd values
detected with < 2 dimensions.Warning: Assuming temperature.Warning: New
style (Amber >= V18) remd values detected with < 2 dimensions.Warning:
Assuming temperature.Warning: New style (Amber >= V18) remd values
detected with < 2 dimensions.Warning: Assuming temperature.Warning: New
style (Amber >= V18) remd values detected with < 2 dimensions.Warning:
Assuming temperature.Warning: New style (Amber >= V18) remd values
detected with < 2 dimensions.Warning: Assuming temperature. [trajout
REMD_only_5pH_00001.nc] Writing 'REMD_only_5pH_00001.nc' as Amber
NetCDF---------- RUN BEGIN
-------------------------------------------------PARAMETER FILES (1
total): 0: exp.modO.parm7, 129761 atoms, 42410 res, box: Orthogonal, 42185
mol, 41941 solventINPUT TRAJECTORIES (1 total): 0: REMD trajectories (8
total), lowest replica 'exp_remd_pH2_5_00001.nc.000' (reading 5000 of
5000) Looking for frames at 5.00 K Coordinate processing will occur
on 5000 frames.*
*OUTPUT TRAJECTORIES (1 total): 'REMD_only_5pH_00001.nc' (5000 frames) is
a NetCDF AMBER trajectoryBEGIN TRAJECTORY
PROCESSING:....................................................ACTIVE
OUTPUT TRAJECTORIES (1): REMD_only_5pH_00001.nc (coordinates, temperature,
time, replica indices, coordinate indices, box)-----
exp_remd_pH2_5_00001.nc.000 (1-5000, 1) ----- 0% 10% 20% 30% 40% 50% 60%
70% 80% 90% 100% Complete.Read 5000 frames and processed 5000 frames.TIME:
Avg. throughput= 40.0985 frames / second.ACTION OUTPUT:TIME: Analyses took
0.0000 seconds."*
And everything looks fine, except lines
*"Warning: New style (Amber >= V18) remd values detected with < 2
dimensions.*
*Warning: Assuming temperature" *
I would like to ask, if the warnings are normal for the pH-REMD?
Best regards,
Elvira.
чт, 15 нояб. 2018 г. в 22:15, Daniel Roe <daniel.r.roe.gmail.com>:
> 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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>
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Received on Thu Nov 15 2018 - 20:30:01 PST
