Also keep in mind that PDB residue numbering does not necessarily
match up with topology residue numbering. By convention Amber will
number residues starting from 1 to N, where N is the total number of
residues in the system. Unless your PDB also has the first residue as
residue 1 and then increases by 1 each residue, the numbering may not
match up.
If you've added PDB information to your topology (with e.g. parmed) or
you are using a PDB file with the original residue numbering as your
topology you can specify using the original (PDB) residue numbering
with the ':;' (colon semicolon) operator instead of ':' (colon).
If you still can't figure it out you'll have to provide me with some
files I can use to try and reproduce whatever issue. Also, let me know
the version of cpptraj you are using.
-Dan
On Fri, May 16, 2025 at 12:59 PM Michael Shokhen via AMBER
<amber.ambermd.org> wrote:
>
> ________________________________
> From: Michael Shokhen <michael.shokhen.biu.ac.il>
> Sent: Friday, May 16, 2025 7:34 PM
> To: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] There seems to be a bug in the CPPTRAJ software
>
> Hi Dan,
>
> Many thanks for your fast response.
> Following your advise I used the "noimage" keyword.
> Unfortunately, it doesn't help.
> See the attached files.
>
> 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>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Friday, May 16, 2025 7:08 PM
> To: Michael Shokhen <michael.shokhen.biu.ac.il>; AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] There seems to be a bug in the CPPTRAJ software
>
> 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://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwebmail.biu.ac.il%2Fowa%2Fredir.aspx%3FC%3Da160ef9b9a6b4d06992402715d3ee465%26URL%3Dmailto%253ashokhen%2540mail.biu.ac.il&data=05%7C02%7Cmichael.shokhen%40biu.ac.il%7Cb625837db20e4d0b682208dd9493fb84%7C61234e145b874b67ac198feaa8ba8f12%7C0%7C0%7C638830085567988715%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=gm20iN9kpyub9gFimFfUcJKNkpfASRyjacbc2OfYizg%3D&reserved=0>
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Received on Fri May 16 2025 - 11:30:03 PDT
