Dear AMBER Experts,
This is regarding calculating the center of mass coordinates of protein,
with CPPTRAJ.
I have basically followed the CPPTRAJ section of the AMBER Manual as
follows:
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
#centering
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
Vec_00002[Mag]
1 -5.1339 -46.4399 4.2386 0.0000 0.0000 0.0000
46.915
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
0
Info) Finished with coordinate file DM_1_000050.pdb.
vmd > set a [atomselect top "protein and resid 1 to 43"]
atomselect0
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,
Regards,
Prathit Chatterjee
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Received on Thu Aug 27 2020 - 05:00:02 PDT
