Dear Amber users,
I used following command to convert AMBER 12 generated
rst-file [*test_equil.rst
*having one frame, netCDF format ] to pdb:
cpptraj -i ptraj_input -p test1_sol.prmtop
where input file *[ptraj_input] *consists of following:
trajin
test_equil.rst
trajout test_equil_rst.pdb pdb nobox append
go
and *test1_sol.prmtop* is the parameter topology file.*
*I got the following error message instead of getting output
[*test_equil_rst.pdb
*]
Error: CpptrajFile::SetupFile: NULL filename specified on READ or APPEND
Error: Could not set up file test_equil_rst.pdb for writing.
Error: trajout: Could not set up trajectory.
*May I have to alter **input file [ptraj_input] for netCDF format?*
I also tried the following:
ambpdb -p *test1_sol.prmtop* < *test_equil.rst* > * test_equil_rst.pdb
*In this case, I got the output in pdb format with following message: *New
format PARM file being parsed*.
| Version = 1.000 Date = 07/06/12 Time = 15:32:11*
*But, the two calcium atoms it binds could not be visualised ; the pdb file
format of the test_equil_rst.pdb looks fine.
Thanks,
Mahendra Thapa
University of Cincinnati
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Received on Mon Jul 30 2012 - 10:00:05 PDT
