Hi,
On Sat, Aug 12, 2023 at 4:42 AM m.bzowka m.bzowka via AMBER <
amber.ambermd.org> wrote:
>
> My problem is that when I process the trajectory file with cpptraj and
> when I open the .nc file in vmd, I can't see the three non-standard
> residues in the sequence and I observe the gaps in the structure. Also,
> when I performed the rmsf analysis of the trajectory, in the output file
> there is no rmsf value for these three residues.
Cpptraj will never modify a topology without explicitly being told to. I’m
not sure what’s going on with VMD (I assume you are using the stripped
topology when you visit the stripped trajectory right?) but as far as the
RMSF not selecting your 3 nonstandard residues, are you certain of your
residue numbering after the ‘strip’ command? The ‘:’ selector goes by
absolute residue numbering, which can change after ‘strip’.
I noticed in the output file from the cpptraj the following warnings:
> Warning: 1 molecules have non-contiguous segments of atoms.
> 1 2 segments: 1-6865 (6865) 12658-19658 (7001)
> Warning: The 'fixatomorder' command can be used to reorder the topology
> and any
> Warning: associated coordinates.
This warning in older versions of cpptraj would just mean there would be no
molecule information available. In more recent versions its more of an FYI.
It shouldn’t be impacting the analysis your are doing. What cpptraj version
are you using? You should use AmberTools23 or GitHub if you can.
#autoimage
> center :1-1255 mass origin
> image origin center familiar
Did autoimage not work for you here?
> strip :WAT,Cl-,Na+ outprefix nowat
This can potentially change ‘:’ mask numbering. ‘:;’ numbering should
remain unchanged.
> trajout *_nowat.nc NetCDF
The asterisk in trajout is worrisome. You should be providing a filename
here. The behavior here is undefined - at best I think it will overwrite
the first matching file.
> go
> Attached, please find the .out file from cpptraj.
There was no attachment. Maybe you can send it to me directly off-list.
-Dan
>
> Thank you in advance for your help.
>
> Best
> Maria Bzówka
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Received on Sat Aug 12 2023 - 06:00:02 PDT
