It looks like you are centering and imaging in cpptraj but not in vmd, so
why would they match? Maybe I’m not exactly understanding the issue you're
having.
On Thu, Aug 27, 2020 at 7:59 AM Prathit Chatterjee <
prathit.biophysics.gmail.com> wrote:
> 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
>
> _______________________________________________
>
> AMBER mailing list
>
> AMBER.ambermd.org
>
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 04 2020 - 11:30:02 PDT
