Hi, and thanks for the files!
So I figured out why CPPTRAJ wasn't picking up the non-standard
residues. You're using masks like :
1-1255.CA and :
1-1255.CA,C,N, but
the nonstandard residues have atom names like C2, C3, etc. So for
selecting the equivalent of CA atoms, for the SSP residue it looks
like you would want C2 and for RPA it looks like you want C3 (you may
want to double check me on that, I only glanced at it briefly). So you
would change that rmsf command to:
atomicfluct out rmsf_CA_100ns_x1.arg :
1-1255.CA,C2,C3 byres
You'll have to do the same for the backbone atom one (figure out the
equivalent atoms of C and N, for SSP it lookslike C3 and C4 and for
RPA it looks like C8 and N1 but again, double check).
On Sat, Aug 12, 2023 at 9:44 AM Maria Bzówka <m.bzowka.tunnelinggroup.pl> wrote:
>
> When I wanted to check the residues numbering I noticed that when in cpptraj I used the command:
> atoms ^1
> Information about all amino acids starting from 1, ending at 424 (that's part of the receptor from the beginning to the residue after which the cleavage takes place) and starting from 786 and ending at 1255 appeared (that's part of the protease).
The carat (^) character means "select by molecule number", i.e. where
a "molecule" is all atoms connected by bonds. So ^1 selects all atoms
in molecule 1. The residue numbering (1-424, 786-1255) is the internal
residue numbering (i.e. the order in which those residues appear in
the topology), which is why you get the warning about the molecule
having non-contiguous residues.
> Regarding your other questions; I commented autoimage option because I didn't see any difference in my output .nc file, whether it was used or not. Should I keep the autoimage option? I also used the whole names of the files and the results were the same. And yes, in the vmd I was loading the stripped topology.
The issue is that the subsequent 'image' and 'center' commands
effectively overwrite 'autoimage', so either use 'autoimage' (which I
recommend because it usually does a better job than separate image or
center) or 'center'/'image'.
Let me know if this clears things up or if you have more questions.
Thanks again for the files!
-Dan
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Received on Sat Aug 12 2023 - 18:00:02 PDT
