Hi,
First, I recommend using cpptraj from AmberTools 14. It is the most stable
and up-to-date version.
On Sat, Jul 5, 2014 at 3:48 AM, Mele N. <nm10g13.soton.ac.uk> wrote:
> Found 80 replicas.
> [remd.mdcrd.001] contains 551 frames.
> Warning: RemdTraj: Replica remd.mdcrd.002 frames (552) does not match
> Warning: # frames in first replica (551).
>
Is this from a run which crashed unexpectedly? Definitely use cpptraj V14 -
it handles malformed replica ensembles much more gracefully. The other
reason you would get this message is if the topology you are using doesn't
match your coordinates (e.g. you are using a solvated topology with
stripped coordinates).
> Error: RemdTraj: Replica remd_r2.mdcrd.001 does not have temperature info.
> Error: trajin: Could not set up trajectory.
>
Are you using ASCII or NetCDF trajectories?
-Dan
>
>
> I don't know what is happening with my run after the first one, it is like
> the files are not recognized.
> It is really strange, because with another system everything goes right. I
> used Replica exchange in two different system with the same input file but
> here I get this error.
> I used as input file for the analysis this file:
>
> #!/bin/bash
>
> cpptraj AVP_open.prmtop <<EOF
> trajin remd.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r2.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r3.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r4.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r5.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r6.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r7.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r8.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r9.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r10.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r11.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r12.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r13.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r14.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r15.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r16.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r17.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r18.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajin remd_r19.mdcrd.001 remdtraj remdtrajtemp 302.28
>
> trajout remd_300K.mdcrd nobox
> go
> EOF
>
>
> I am so confused,
>
> Do you have any idea?
>
> Thank you in advance,
>
> Nawel
> ________________________________________
> De : Mele N. [nm10g13.soton.ac.uk]
> Envoyé : vendredi 4 juillet 2014 21:22
> À : AMBER Mailing List
> Objet : Re: [AMBER] ptraj: Could not find target 302.280000 in any of the
> replica trajectories
>
> Thanks you very much for your help,
> I will try it tomorrow and let you know if it work.
>
> ________________________________________
> De : Jason Swails [jason.swails.gmail.com]
> Envoyé : vendredi 4 juillet 2014 20:58
> À : AMBER Mailing List
> Objet : Re: [AMBER] ptraj: Could not find target 302.280000 in any of the
> replica trajectories
>
> On Fri, Jul 4, 2014 at 12:23 PM, Mele N. <nm10g13.soton.ac.uk> wrote:
>
> > Thanks a lot for your answer,
> >
> > Actually I have a number of run for each replica, so you mean that just
> by
> > providing the lowest replica it will recognized even all the different
> run?
> >
>
> No. You need to provide the lowest replica number for _each_ run on a
> separate trajin or ensemble line.
>
>
> >
> > By the way I used amber12 , does it change the way to analyse the
> > temperature trajectories compare to Amber14?
> >
>
> No difference.
>
> For example:
>
> trajin run1.mdcrd.000
> trajin run2.mdcrd.000
> trajin run3.mdcrd.000
> ...
>
> Assuming you named your files run1.mdcrd.000, run1.mdcrd.001,
> run.mdcrd.002, ... etc for the first run and then changed "run1" to "run2"
> for the second run, etc.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sat Jul 05 2014 - 08:00:04 PDT
