Dear Users,
I have a trajectory file and/or pdb file. How can I calculate the
protonation state (singly or doubly protonated) of a particular residue
from trajectory or pdb file?
I am trying to find the problem using the cpptraj cphstats command. But it
give the following error.
parm *.prmtop
trajin ph5.nc
cphstats deprot fracplotout p1.out
go
INPUT: Reading input from 'test.in'
[parm ../ambercpin.prmtop]
Reading '../ambercpin.prmtop' as Amber Topology
Radius Set: H(N)-modified Bondi radii (mbondi2)
[trajin ../ph5_autoimage.nc 1 1]
Reading '../ph5_autoimage.nc' as Amber NetCDF
[cphstats deprot fracplotout p1.out]
Warning: 'fracplotout' selects no data sets.
Warning: 'p1.out' selects no data sets.
Error: No pH data sets.
Error: Could not setup analysis [cphstats]
1 errors encountered reading input.
TIME: Total execution time: 0.0769 seconds.
Error: Error(s) occurred during execution.
Thanking you
--
*With regards,*
*Dulal Mondal,*
*Research Scholar,*
*Department of Chemistry,*
*IIT Kharagpur, Kharagpur 721302.*
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Received on Sat Apr 29 2023 - 10:00:02 PDT
