So, I am trying to make CPPTRAJ do something it was probably not intended to do in order to create input files for another piece of software.
This is the command that I am attempting to execute:
ambmask -p *.prmtop -c nvt10ns.rst -out pdb -find '(:1)’
When I am doing this on a simulation where both RST and CRD files are binary (NETCDF) I get this error:
| New format PARM file being parsed.
| Version = 1.000 Date = 01/30/18 Time = 11:33:27
natom = 21616
nres = 2149
STOP error reading natom from inpcrd
When trying to do the same on a simulation that wrote the RST files in ASCII it works. Naively I though that a simple conversation a la:
cpptraj -p *.prmtop -y nvt10ns.rst -x nvt10ns_ascii.rst
Would fix this however it did not. I do notice that there are slight differences, the ascii written RST file has the following first lines:
default_name
21616 0.1230000E+05
Whereas this information is missing in the converted file, along with what I am assuming is the box side angles on the last row.
So, I would prefer not having to manually edit all of the files I need to be able to perform the task at hand, can I somehow get this information included when converting formats so that I can get the expected output from ambmask?
Best regards
// Gustaf
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Received on Thu Aug 30 2018 - 05:30:05 PDT
