Hi,
On Thu, Jun 1, 2023 at 2:38 AM Maria Bzówka via AMBER <amber.ambermd.org> wrote:
>
> First of all, in the created .crd and .prmtop files we have the protein,
> 1Na, 3Ca, only 2Cl molecules (so the numbering for the small molecules has
> changed and three Cl ions were somehow excluded - we don't know why) and
> later the closest water molecules.
By default, 'closest' should be keeping the N closest solvent
molecules and anything else not solvent. It shouldn't be removing
anything else. I would need to see your complete cpptraj output or
have access to your topology and a single coordinate frame before I
could try to figure out why this apparently isn't happening for you.
One thing you can try is to explicitly select the solvent using the
'solventmask' keyword.
> In the example below we can see that a water molecule with an index 67 was
> found in the first frame - how to get its real index? Should we add the
Not sure what you mean here by it's "real" index. The [Mol] column has
molecule numbers (starting from 1), and the [FirstAtm] keyword has the
number of the first atom in the molecule (again starting from 1); you
can use cpptraj to get more details on that water using the 'atoms'
command, e.g.
parm FS.prmtop
atoms ^67
Hope this helps,
-Dan
> number of protein residues or also other small molecules? If so what about
> those ions which were excluded during the analysis?
>
>
> Below you can find both the input file command as well as output .dat file.
> input.in
> parm FS.prmtop
> reference FS.inpcrd
>
> trajin x1.nc
> autoimage
> center :1-1255 mass origin
>
> closest 5 :870.NE2 first closestout out.dat outprefix 5closest
> trajout out.crd
>
> go
>
> output.dat
> #CLOSEST_00002[Frame] CLOSEST_00002[Mol] CLOSEST_00002[Dist]
> CLOSEST_00002[FirstAtm]
> 1 10168 3.2605
> 50142
> 1 9848 4.5560
> 49182
> 1 6826 4.6368
> 40116
> 1 5117 5.4421
> 34989
> 1 67 6.4906
> 19839
>
> Thank you in advance for your help.
>
> Best regards
> Maria Bzówka
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Received on Thu Jun 01 2023 - 11:00:03 PDT
