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Protein center of mass and urea rdf
#37537 06/26/19 12:06 PM
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Rohit Offline OP
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Hi,

I wanted to calculate rdf for center of mass of urea and center of mass of protein
below is the snippet I am using. this code gives me rdf first peak position at 1 Angs.
what is wrong with the code. it should not have given me peak at 1 angs. kindly help.

Code:
! g(r) for the UREA with Center of mass of protein 
coor anal select segid UREA end -
      site select segid PRT show end -
      firstu 21 nunit 1 skip 1 -     ! trajectory specification
      igdist 68 -                    ! flag to do the solvent-solvent g(r)
      mgn 100 dr 0.1 -               ! comp. g(r) at MGN points separated by DR
      rsph 999.9  -                  ! we use ALL waters for the calculation
      xbox @6 ybox @7 zbox @8        ! and we did use PBC


data from rdf snippet. as you can see 0.10000E+01 0.28029E+02 0.10691E+01 peak position is at 1 angs.
Code:
   0.10000E+00 0.24689E+00 0.18962E-03
   0.20000E+00 0.34937E+00 0.91796E-03
   0.30000E+00 0.40061E+00 0.25443E-02
   0.40000E+00 0.43159E+00 0.54330E-02
   0.50000E+00 0.44956E+00 0.99218E-02
   0.60000E+00 0.46360E+00 0.16382E-01
   0.70000E+00 0.47467E+00 0.25184E-01
   0.80000E+00 0.48173E+00 0.36654E-01
   0.90000E+00 0.48874E+00 0.51186E-01
   0.10000E+01 0.28029E+02 0.10691E+01
   0.11000E+01 0.49911E+00 0.10909E+01
   0.12000E+01 0.44913E+01 0.13220E+01
   0.13000E+01 0.80824E+01 0.18071E+01
   0.14000E+01 0.18090E+01 0.19323E+01
   0.15000E+01 0.51574E+00 0.19731E+01
   0.16000E+01 0.73802E+00 0.20393E+01
   0.17000E+01 0.33701E+01 0.23791E+01
   0.18000E+01 0.27843E+01 0.26929E+01
   0.19000E+01 0.27009E+01 0.30310E+01
   0.20000E+01 0.61860E+01 0.38869E+01
   0.21000E+01 0.26006E+01 0.42827E+01
   0.22000E+01 0.37405E+01 0.49061E+01
   0.23000E+01 0.39008E+01 0.56153E+01
   0.24000E+01 0.22401E+01 0.60579E+01
   0.25000E+01 0.21075E+01 0.65091E+01
   0.26000E+01 0.15044E+01 0.68569E+01
   0.27000E+01 0.11863E+01 0.71522E+01
   0.28000E+01 0.12458E+01 0.74854E+01
   0.29000E+01 0.13548E+01 0.78735E+01
   0.30000E+01 0.19700E+01 0.84768E+01
   0.31000E+01 0.35380E+01 0.96325E+01
   0.32000E+01 0.24448E+01 0.10483E+02
   0.33000E+01 0.21429E+01 0.11274E+02
   0.34000E+01 0.20016E+01 0.12058E+02
   0.35000E+01 0.18792E+01 0.12838E+02
   0.36000E+01 0.18935E+01 0.13668E+02
   0.37000E+01 0.19339E+01 0.14564E+02
   0.38000E+01 0.20259E+01 0.15552E+02
   0.39000E+01 0.22126E+01 0.16689E+02
   0.40000E+01 0.21040E+01 0.17825E+02
   0.41000E+01 0.19701E+01 0.18942E+02
   0.42000E+01 0.19533E+01 0.20103E+02
   0.43000E+01 0.19429E+01 0.21313E+02
   0.44000E+01 0.19325E+01 0.22573E+02
   0.45000E+01 0.19232E+01 0.23884E+02
   0.46000E+01 0.19204E+01 0.25250E+02
   0.47000E+01 0.19204E+01 0.26677E+02
   0.48000E+01 0.19210E+01 0.28164E+02
   0.49000E+01 0.19200E+01 0.29713E+02
   0.50000E+01 0.19161E+01 0.31321E+02
   0.51000E+01 0.19106E+01 0.32990E+02
   0.52000E+01 0.19065E+01 0.34719E+02
   0.53000E+01 0.19026E+01 0.36512E+02
   0.54000E+01 0.18974E+01 0.38367E+02
   0.55000E+01 0.18924E+01 0.40286E+02
   0.56000E+01 0.18867E+01 0.42268E+02
   0.57000E+01 0.18787E+01 0.44313E+02
   0.58000E+01 0.18677E+01 0.46417E+02
   0.59000E+01 0.18539E+01 0.48577E+02
   0.60000E+01 0.18389E+01 0.50793E+02
   0.61000E+01 0.18256E+01 0.53066E+02
   0.62000E+01 0.18158E+01 0.55401E+02
   0.63000E+01 0.18082E+01 0.57801E+02
   0.64000E+01 0.18027E+01 0.60270E+02
   0.65000E+01 0.17985E+01 0.62810E+02
   0.66000E+01 0.17946E+01 0.65422E+02
   0.67000E+01 0.17915E+01 0.68109E+02
   0.68000E+01 0.17891E+01 0.70872E+02
   0.69000E+01 0.17867E+01 0.73713E+02
   0.70000E+01 0.17856E+01 0.76634E+02
   0.71000E+01 0.17841E+01 0.79637E+02
   0.72000E+01 0.17819E+01 0.82720E+02
   0.73000E+01 0.17796E+01 0.85884E+02
   0.74000E+01 0.17770E+01 0.89131E+02
   0.75000E+01 0.17751E+01 0.92462E+02
   0.76000E+01 0.17732E+01 0.95877E+02
   0.77000E+01 0.17712E+01 0.99379E+02
   0.78000E+01 0.17693E+01 0.10297E+03
   0.79000E+01 0.17669E+01 0.10664E+03
   0.80000E+01 0.17641E+01 0.11041E+03
   0.81000E+01 0.17615E+01 0.11426E+03
   0.82000E+01 0.17587E+01 0.11820E+03
   0.83000E+01 0.17554E+01 0.12223E+03
   0.84000E+01 0.17521E+01 0.12635E+03
   0.85000E+01 0.17488E+01 0.13055E+03
   0.86000E+01 0.17454E+01 0.13485E+03
   0.87000E+01 0.17417E+01 0.13924E+03
   0.88000E+01 0.17382E+01 0.14372E+03
   0.89000E+01 0.17343E+01 0.14830E+03
   0.90000E+01 0.17303E+01 0.15296E+03
   0.91000E+01 0.17269E+01 0.15772E+03
   0.92000E+01 0.17233E+01 0.16257E+03
   0.93000E+01 0.17198E+01 0.16752E+03
   0.94000E+01 0.17166E+01 0.17257E+03
   0.95000E+01 0.17132E+01 0.17771E+03
   0.96000E+01 0.17100E+01 0.18295E+03
   0.97000E+01 0.17067E+01 0.18829E+03
   0.98000E+01 0.17037E+01 0.19374E+03
   0.99000E+01 0.17007E+01 0.19928E+03
   0.10000E+02 0.16977E+01 0.20492E+03




Thnak-you,
Regards,
Rohit Modee

Last edited by Rohit; 06/26/19 12:07 PM.
Re: Protein center of mass and urea rdf
Rohit #37538 06/26/19 05:22 PM
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rmv Online Content
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COOR ANAL is mostly intended for solvent analysis.

I don't think COOR ANAL is doing what you want here; you probably need to use an atom close to the center of mass of each molecule as a surrogate to get something that approximates your goal.

Also, you probably want ISDIST instead of IGDIST.


Rick Venable
computational chemist

Re: Protein center of mass and urea rdf
rmv #37540 06/27/19 07:45 AM
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Originally Posted By: rmv
COOR ANAL is mostly intended for solvent analysis.

so is their any other module for solute-solvent rdf analysis?



Originally Posted By: rmv
Also, you probably want ISDIST instead of IGDIST.

In corman ISDIST and IGDIST are said to be mutually exclusive.
ISDIST is for sites if I am not wrong. so what is IGDIST for there is no clear explanation for IGDIST in corman. Can you please elaborate on IGDIST.

Re: Protein center of mass and urea rdf
Rohit #37541 06/27/19 03:42 PM
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See the second and third examples. The second example indicates IGDIST generates water:water g(r) for O:O, O:H, and H:H pairings. The third example (using ISDIST) computes g(r) for water oxygens around the backbone amide H atoms.

The g(r) facility in COOR ANAL is tailored to evaluate atom pairings, so you could look at e.g. the urea O atom around the Lys and/or Arg, or urea N atoms around Asp or Glu. To avoid overcounting, it is advised to use a single atom for cases like carboxylate and guanidinium groups, such as the central C atom in each of these moieties.

An alternative is the COOR DIST approach, which allows far greater flexibility in defining the distance pair, but is slower as it involves a loop over frames in the CHARMM input script. You need to take more care with image atoms, performing an UPDATE command after reading each frame with the IMALL keyword, with CUTIM set to the same value as the CUT option of COOR DIST. The COOR DIST command must also include the IMAGE keyword. You can also preprocess the trajectory to center the protein, so that it is never too close to edge of the box, and not have to worry about image atoms.




Rick Venable
computational chemist

Re: Protein center of mass and urea rdf
Rohit #37544 06/29/19 08:39 AM
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IGDIST is for solvent-solvent g(r); you only need one selection:
coor anal water select type OH2 end -
firstu 21 nunit 1 skip 10 - ! trajectory specification
igdist 31 ioh 32 ihh 33 - ! flag to do the solvent-solvent g(r)
mgn 100 dr 0.1 - ! comp. g(r) at MGN points separated by DR
rsph 999.9 - ! use ALL waters for rdf calculation
xbox @6 ybox @7 zbox @8 ! and we did use PBC

ISDIST is as you say for g(r) of solute (site(s)) vs solvent, and is what you should use:
! g(r) backbone amide hydrogen - water oxygens
! if a single solute atom is looked at the MULTi keyword is not necessary
! when several solute atoms are specified as the site, their average position
! will be used as the reference position if MULTi is not present
open unit 21 read unform name @9pept500.cor
open unit 31 write form name @9pept500.gonh
coor anal select type oh2 end - ! Water oxygens
site select type H end multi - ! and the amide hydrogens
firstu 21 nunit 1 skip 10 - ! trajectory specification
isdist 31 - ! do the g(r) (here solute-solvent)
mgn 100 dr 0.1 - ! comp. g(r) at MGN points separated by DR
rsph 999.9 - ! we use ALL waters for the calculation
xbox @6 ybox @7 zbox @8 ! and we did use PBC


The complication in your case is that COOR ANAL does not allow you to specify that the center of mass of each urea molecule should be used. A work-around is to pick an atom close to the center of mass: sele resn urea .and. type C2 end




Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Protein center of mass and urea rdf
Rohit #37545 06/29/19 10:37 AM
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Rohit Offline OP
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Thank-you for clarification.


Moderated by  BRBrooks, lennart, rmv 

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