Michael,
‘noimage’ is a keyword for the ‘distance’ command; not a separate command.
There was an example in the script I sent you.
In general, it is recommended that you read the manual entries for all
commands you are going to be using.
Hope this helps,
-Dan
On Mon, May 19, 2025 at 3:35 PM Michael Shokhen <michael.shokhen.biu.ac.il>
wrote:
> Hi Dan,
> Thanks for your reply. You provided the CA-CA distances between Asp923 and
> Ala1479,
> calculated from the three PDB files I sent you earlier, as you requested.
> You demonstrated that by using the "noimage" keyword in the script to run
> CPPTRAJ,
> you indeed calculated the correct values of the large distances.
> Following your advice,
> I used the "noimage" keyword in my "cpptr_dist.in" script to calculate
> the distances
> of a 5 ns MD trajectory containing 2500 snapshots. See the attached script
> and
> the corresponding CPPTRAJ results in the AGR file. Unfortunately, the
> "noimage" keyword
> did not solve the problem - all the distances are wrong, as I wrote to you
> earlier.
> Could you please correct my commands in the script and send them to me so
> that I can apply
> them to calculate the correct distance values. I will keep you updated on
> the results.
>
> Thank you,
> Michael.
>
>
>
>
> ------------------------------
> *From:* Daniel Roe <daniel.r.roe.gmail.com>
> *Sent:* Monday, May 19, 2025 8:45 PM
> *To:* Michael Shokhen <michael.shokhen.biu.ac.il>; AMBER Mailing List <
> amber.ambermd.org>
> *Subject:* Re: [AMBER] Fw: There seems to be a bug in the CPPTRAJ software
>
> Hi,
>
> Thanks for the files.
>
> I looked into this in-depth, and cpptraj is calculating the distances
> properly. The by-hand calculated distances match the ones calculated
> by cpptraj with imaging off. If I omit the 'noimage' keyword for
> 'distance' I get the shorter distance that you reported, which is also
> correct but is the minimum imaged distance (as I stated before). I
> will attach the script I used to test everything and paste the output
> below.
>
> So to sum up, make sure you specify the 'noimage' keyword to the
> 'distance' command if what you want is the non-imaged distance.
>
> -Dan
>
> [droe.de6 2025-05-19_Distance] (master)$ ./Test.sh eq_snapshot_1.pdb
> ATOM 14005 CA ASP 923 -47.876 63.644 13.297 1.00
> 0.00 C
> ATOM 22425 CA ALA 1479 111.241-129.062-121.078 1.00
> 0.00 C
> Info: Redirecting output to file 'cpptraj1.out'
> #Frame ASP923
> 1 -47.8760 63.6440 13.2970 0.0000 0.0000 0.0000
> #Frame ALA1479
> 1 111.2410 -129.0620 -121.0780 0.0000 0.0000 0.0000
> -47.8760 63.6440 13.2970
> 111.2410 -129.0620 -121.0780
> Sum= 80510.46275000
> Dist= 283.74365675729210916086
> #Frame d1
> 1 283.7437
> #Frame d1imaged
> 1 164.9428
> [droe.de6 2025-05-19_Distance] (master)$ ./Test.sh eq_snapshot_1000.pdb
> ATOM 14005 CA ASP 923 -50.609 64.766 15.226 1.00
> 0.00 C
> ATOM 22425 CA ALA 1479 117.407-129.156-107.371 1.00
> 0.00 C
> Info: Redirecting output to file 'cpptraj1.out'
> #Frame ASP923
> 1 -50.6090 64.7660 15.2260 0.0000 0.0000 0.0000
> #Frame ALA1479
> 1 117.4070 -129.1560 -107.3710 0.0000 0.0000 0.0000
> -50.6090 64.7660 15.2260
> 117.4070 -129.1560 -107.3710
> Sum= 80865.14274900
> Dist= 284.36797068059546146633
> #Frame d1
> 1 284.3680
> #Frame d1imaged
> 1 162.9013
> [droe.de6 2025-05-19_Distance] (master)$ ./Test.sh eq_snapshot_2500.pdb
> ATOM 14005 CA ASP 923 -52.292 65.593 25.838 1.00
> 0.00 C
> ATOM 22425 CA ALA 1479 116.039-138.392-131.288 1.00
> 0.00 C
> Info: Redirecting output to file 'cpptraj1.out'
> #Frame ASP923
> 1 -52.2920 65.5930 25.8380 0.0000 0.0000 0.0000
> #Frame ALA1479
> 1 116.0390 -138.3920 -131.2880 0.0000 0.0000 0.0000
> -52.2920 65.5930 25.8380
> 116.0390 -138.3920 -131.2880
> Sum= 94633.78566200
> Dist= 307.62604841267912369646
> #Frame d1
> 1 307.6260
> #Frame d1imaged
> 1 139.3277
>
> On Sun, May 18, 2025 at 1:21 AM Michael Shokhen via AMBER
> <amber.ambermd.org> wrote:
> >
> > Hi Dan,
> >
> > As per your request, I am sending you a compressed ZIP file of the
> topology. I have also generated three PDB files corresponding to the MD
> trajectory snapshots: 1, 1000 and 2500.
> > These compressed ZIP files are each 30.7 MD in size, so I am sending
> them in three separate emails. Please let me know if I have missed any of
> the requested data and I will send them to you.
> >
> > All the best,
> > 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%7C3733299401814dd84fc408dd96fcf4bc%7C61234e145b874b67ac198feaa8ba8f12%7C0%7C0%7C638832735617618948%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C80000%7C%7C%7C&sdata=H%2FYFT8uM5oWGz7bW8uIyKOAOxMXY%2FNdcJY7hOOF1svE%3D&reserved=0
> >
>
> > ________________________________
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Sent: Saturday, May 17, 2025 4:52 PM
> > To: Michael Shokhen <michael.shokhen.biu.ac.il>
> > Cc: amber.ambermd.org <amber.ambermd.org>
> > Subject: Re: [AMBER] Fw: There seems to be a bug in the CPPTRAJ software
> >
> > Hi,
> >
> > No need for something so elaborate. Just send me off-list the topology
> > and a few trajectory frames which illustrate the issue. Let me know if
> > you need help generating the smaller trajectory.
> >
> > -Dan
> >
> > On Sat, May 17, 2025 at 7:54 AM Michael Shokhen
> > <michael.shokhen.biu.ac.il> wrote:
> > >
> > > Hi Dan,
> > >
> > > I am using the AMBR24 package which includes the CPPTRAI software.
> > > I could not determine the version number of the latter.
> > > In the PDB file, the first residue of the protein is residue #1 and
> then
> > > the numbering of the protein residues increases by 1 until the last
> residue
> > > is #1488 followed by the solvent components: 1382 Na+, 1394 Cl- and
> Wat 51544 Wat.
> > > The whole system contains 1571688 atoms.
> > > Thank you very much for your kind offer to identify the CPPTRAJ
> problem I was facing.
> > > In order to provide you with the required files, I have collected them
> in one directory.
> > > I am using AWS cloud server for AMBER24 calculations. The whole system
> is quite large,
> > > so the total directory I have prepared for submission is 47.6 GB.
> > > Next week, I will ask the AWS system manager to prepare the password
> and instruction
> > > on how you can download the files form AWS server. I will send you the
> details to your email.
> > >
> > > Thanks again,
> > > Michael
> > >
> > > ________________________________
> > > From: Daniel Roe <daniel.r.roe.gmail.com>
> > > Sent: Friday, May 16, 2025 9:04 PM
> > > To: Michael Shokhen <michael.shokhen.biu.ac.il>; AMBER Mailing List <
> amber.ambermd.org>
> > > Subject: Re: [AMBER] Fw: There seems to be a bug in the CPPTRAJ
> software
> > >
> > > 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://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%7C3733299401814dd84fc408dd96fcf4bc%7C61234e145b874b67ac198feaa8ba8f12%7C0%7C0%7C638832735617655353%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C80000%7C%7C%7C&sdata=r%2F%2FjKEmh3GJejfkur5sF6Ibh1r8g6uHVH30aJ3%2FQ2OM%3D&reserved=0
> >
>
> > > > ________________________________
> > > > 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<
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> > > > > _______________________________________________
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Received on Tue May 20 2025 - 09:30:02 PDT
