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://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: 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%7C332c958aab2d4f19484208dd954a261a%7C61234e145b874b67ac198feaa8ba8f12%7C0%7C0%7C638830867886413362%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=othBD3MunwCAb0jPrLrUdJXs8AIWesCkOe13%2FLriln0%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<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%7C332c958aab2d4f19484208dd954a261a%7C61234e145b874b67ac198feaa8ba8f12%7C0%7C0%7C638830867886432026%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=y6KcIZ4hvFGGKd0ZB73VOzhyjgMQAzgpm5STWLwT7Is%3D&reserved=0>
> > > _______________________________________________
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Received on Sat May 17 2025 - 22:30:02 PDT
