[AMBER] Confusion regarding Center of mass coordinates for protein, with CPPTRAJ

From: Prathit Chatterjee <prathit.biophysics.gmail.com>
Date: Thu, 27 Aug 2020 20:58:48 +0900

Dear AMBER Experts,

This is regarding calculating the center of mass coordinates of protein,

I have basically followed the CPPTRAJ section of the AMBER Manual as
vector [<name>] <Type> [out <filename> [ptrajoutput]] [<mask1>] [<mask2>]
[magnitude] [ired]
<Type> = { mask | minimage | dipole | center | corrplane |
box | boxcenter | ucellx | ucelly | ucellz
principal [x|y|z] }...
...[magnitude] Store the magnitude of the vector with aspect [Mag].

I have loaded one frame and have tried to calculate it :
parm DM_1.top
reference DM_1_md0000.rst [FIRST]
trajin DM_1_md0001.crd 50 50
strip :WAT
strip :Na+
strip :Cl-
center :1-43 mass origin
image origin center familiar
vector center out com_test9_Tau.dat :1-43 magnitude

The results obtained is as follows:
#Frame Vec_00002
       1 -5.1339 -46.4399 4.2386 0.0000 0.0000 0.0000

But, the same thing which when I try to calculate with vmd for
cross-checking, is giving different results as follows (I am sure about the
technicalities I am using in VMD, and therefore presume the data obtained
from VMD is correct). Please see below:
vmd > mol new DM_1_000050.pdb
Info) Using plugin pdb for structure file DM_1_000050.pdb
Info) Using plugin pdb for coordinates from file DM_1_000050.pdb
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 1288
Info) Bonds: 1300
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 86
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 2 Protein: 2 Nucleic: 0
Info) Finished with coordinate file DM_1_000050.pdb.
vmd > set a [atomselect top "protein and resid 1 to 43"]
vmd > measure center $a weight mass
-0.3192976117134094 -24.074199676513672 0.9994136691093445

I therefore wanted to know whether the CPPTRAJ technical commands I am
using are correct or not, and would want to implement the proper commands
for calculating the center of mass.
Any suggestions in this regard will be deeply appreciated.

Thank you in advance,
Prathit Chatterjee
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Received on Thu Aug 27 2020 - 05:00:02 PDT
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