Hi,
My guess is that the distance calculated by cpptraj is not wrong, it's
just not what you expect. By default, when periodic boundary
conditions are present, cpptraj reports the shortest distance between
the two specific masks according to the minimum image convention (see
the 'distance' command entry in the cpptraj manual). If you don't want
imaged distances, specify the 'noimage' keyword.
Hope this helps,
-Dan
On Fri, May 16, 2025 at 11:45 AM Michael Shokhen via AMBER
<amber.ambermd.org> wrote:
>
> CPPTRAJ in AMBER24 incorrectly calculates the CA-CA distance between amino acid residues in a protein.
> I used the AMBER24 molecular dynamics simulation of a large protein containing 1488 residues. The initial conformation of the protein is very extended. After several standard geometry optimization steps in a periodic rectangular water box also containing Na+ Cl- ions at physiological concentration, I used a short conventional molecular dynamics simulation of 5 ns duration to equilibrate the whole system:
> equilibrate 5ns
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=2500000,dt=0.002,
> ntc=2,ntf=2,ig=-1,
> cut=8.0, ntb=2, ntp=1, taup=2.0,
> ntpr=1000, ntwx=1000,
> ntt=3, gamma_ln=2.0,
> temp0=310.0,
> /
> In the next step, I used the CPPTRAJ script cpptr_dist.in to calculate the CA-CA distance value between residues ASP923 and ALA1479 in the last 2500 snapshot:
>
> # Distance analysis with cpptraj.
> # Load topology trajectory
> parm ../mc.prmtop
> trajin ../6_/eq.mdcrd 2500 2500
> strip :WAT,Cl-,Na+
> autoimage origin
> distance ASP923_ALA1479 :923.CA :1479.CA out dist_CA-CA_ASP923_ALA1479_eq_2500.agr
> run
> The result is as follows:
> with g0
> xaxis label "Frame"
> yaxis label ""
> legend 0.2, 0.995
> legend char size 0.60
> s0 legend "ASP923_ALA1479"
> target G0.S0
> type xy
> 1.000 139.327
>
> I then used the CPPTRAJ script cpptr_pdb.in to generate a PDB file (If needed I'll send the PDB file by request) from the RST file containing the final 3D structure after the 5 ns MD simulation:
>
> parm ../mc.prmtop
> trajin eq.rst
> autoimage origin
> trajout eq_5ns.pdb pdb
> run
> quit
>
> The next two lines contain the XYZ coordinates of the two CA target atoms copied from the PDB file:
>
> ATOM 14005 CA ASP 923 -52.292 65.593 25.838
> ATOM 22425 CA ALA 1479 116.039 -138.392 -131.288
> The target CA-CA distance calculated from PDB coordinates is 307.626 A. The corresponding CA-CA distance value generated by CPPTRAJ is 139.327 A, which is completely wrong!
> There seems to be a bug in the CPPTRAJ software.
> I need to use CPPTRAJ to analyze CA-CA distance variations during long
> MD production simulations.
> I would appreciate help from AMBER experts in fixing this issue.
> Thank you,
> Michael
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: michael.shokhen.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
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Received on Fri May 16 2025 - 09:30:09 PDT
