Hi,
I'm almost certain that you're writing nvt10ns_ascii.rst as an Amber
ASCII trajectory, not a restart file; the recognized extension for
Amber ASCII restarts is '.rst7' (see section 29.9 in the Amber 18
manual or 'help trajout' in cpptraj). Cpptraj will let you know what
format it is writing under 'OUTPUT TRAJECTORIES'.
Also, if what you want to do is create a PDB containing only residue 1
you could just use cpptraj directly:
cpptraj -p *.prmtop -y nvt10ns.rst <<EOF
strip !:1
trajout pdb pdb
EOF
Hope this helps,
-Dan
On Thu, Aug 30, 2018 at 8:20 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> 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 - 06:00:04 PDT
