[AMBER] closest command cpptraj

From: Maria Bzówka via AMBER <amber.ambermd.org>
Date: Thu, 1 Jun 2023 08:38:04 +0200

Dear Amber users,

I wanted to ask for your advice while using the closest command in cpptraj.

The goal was to obtain 5 closest water molecules from a specific atom
within our protein. In the original .pdb and .prmtop files we have 1-1255
protein residues which are followed by 3 Ca, 1Na, 5 Cl molecules and water
molecules (in such order). It seemed that the command worked because we
got both the .dat and .crd file with the information about the closest
residues but we are concerned regarding their numbering (indexing).

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.
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
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.
parm FS.prmtop
reference FS.inpcrd

trajin x1.nc
center :1-1255 mass origin

closest 5 :870.NE2 first closestout out.dat outprefix 5closest
trajout out.crd


#CLOSEST_00002[Frame] CLOSEST_00002[Mol] CLOSEST_00002[Dist]
                    1 10168 3.2605
                    1 9848 4.5560
                    1 6826 4.6368
                    1 5117 5.4421
                    1 67 6.4906

Thank you in advance for your help.

Best regards
Maria Bzówka
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Received on Thu Jun 01 2023 - 00:00:03 PDT
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