Hi,
On Fri, Apr 9, 2021 at 4:39 PM Liao <liaojunzhuo.aliyun.com> wrote:
>
> This behavior I didn’t find someone mention online or in the manual-don’t know if I missed something. One would expect the atom name to correspond to atom name-and the terminal output on screen shows the atoms based on the input names with no mention of the true atoms it’s measuring.
> It’d be great if there’s a way for cpptraj to correspond atom names regardless of their sequence within a residue, otherwise not just atom names, but also atom sequences have to be identical in the initial PDBs from model building, in order to use it to do RMSD and distance calculations.
Yeah, the manual should make this behavior crystal clear. The 'rms'
command (and lots of other commands like it) requires a 1 to 1
correspondence between "reference" atoms and "target" atoms. The order
you specify them in the atom mask does not matter since an atom either
ends up as "selected" or "not selected"; the ordering depends on the
ordering in the respective topology files.
There are two ways around this. The first is to use the 'atommap'
command to try and automatically reorder the atoms to get a 1 to 1
correspondence between reference and target. Be aware that I've really
only tested that on small molecule compounds, not full sized proteins,
although it could work. The second, if you already know the
correspondence between target and reference is to use the 'remap'
command. What is the 'remap' command you ask? It's a command that I
now realize I never added a manual entry for - oops. Here's the
onboard help text (from 'help remap'):
```
remap data <setname> [outprefix <prefix>] [parmout <filename>]
[parmopts <comma-separated-list>]
Re-map atoms according to the given reference data set which is of the format:
Reference[Target]
with atom numbering starting from 1. E.g. Reference[1] = 10 would
mean remap atom 10 in target to position 1.
outprefix <prefix> : Write modified topology to <prefix>.<originalname>
parmout <filename> : Write modified topology to <filename>
parmopts <list> : Options for writing topology file
```
The 'test/Test_Remap' subdirectory has an example of how this command
can be used. I could potentially add a feature to the remap command
that does remapping solely based on atom and/or residue names. If you
send me off-list the PDB files in question I could try to take a stab
at adding that functionality. Also you can add an issue on the cpptraj
GitHub site (
https://github.com/Amber-MD/cpptraj/issues) so the
request doesn't get lost in the shuffle.
Thanks for the report,
-Dan
>
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Received on Mon Apr 12 2021 - 06:30:05 PDT
