Hi,
On Fri, Jul 4, 2014 at 7:19 AM, Mele N. <nm10g13.soton.ac.uk> wrote:
>
> I first concatenate all replica trajectories files:
>
No, this is *not* the correct way to process replica trajectory files. If
your replica trajectories have numerical extensions of fixed length (which
it appears yours do) all you need to provide is the lowest replica; the
other trajectories are found automatically and all replica trajectories are
processed at once to find the target temperature at each frame. There is a
whole section of the Amber 14 manual which covers processing replica
trajectories under the entry '28.1.1. trajin'.
Also, I suggest you switch to cpptraj since it is better-supported. In
addition, there is an 'ensemble' command that lets you process all replica
trajectories at once (so you can e.g. calculate RMSD or strip atoms from
every member of the ensemble at once if desired), as well as greatly
expanded analysis capabilities.
Hope this helps,
-Dan
>
> Here is the scritpt
>
> #!/bin/bash
>
> for R in 001 002 003 004 005 006 007 008 009 010 011 012 013 014 015 016
> 017 018 019 020 021 022 023 024 025 026 027 028 029 030 031 032 033 034 035
> 036 037 038 039 040 041 042 043 044 045 046 047 048 049 050 051 052 053 054
> 055 056 057 058 059 060 061 062 063 064 065 066 067 068 069 070 071 072 073
> 074 075 076 077 078 079 080;
> do
>
> cat remd.mdcrd.$R remd_r2.mdcrd.$R remd_r3.mdcrd.$R remd_r4.mdcrd.$R
> remd_r5.mdcrd.$R remd_r6.mdcrd.$R remd_r7.mdcrd.$R remd_r8.mdcrd.$R
> remd_r9.mdcrd.$R remd_r10.mdcrd.$R remd_r11.mdcrd.$R remd_r12.mdcrd.$R
> remd_r13.mdcrd.$R remd_r14.mdcrd.$R remd_r15.mdcrd.$R remd_r16.mdcrd.$R
> remd_r17.mdcrd.$R remd_r18.mdcrd.$R remd_r19.mdcrd.$R> Remd.mdcrd.$R
>
> done
>
>
>
> And then extract the temperature trajectories.
>
> Here is the script
>
> #!/bin/bash
>
> ptraj AVP_open.prmtop <<EOF
> trajin Remd.mdcrd.001 remdtraj remdtrajtemp 302.28
> trajout remd_302K.mdcrd nobox
> go
> EOF
>
>
> When I run the second script I get this error:
>
> Done.
> 1% ..
> REMDTRAJ: Final repTemp value read= 369.920000, set 590
> Could not find target 302.280000 in any of the replica trajectories.
> Check that all replica trajectory files were found and that
> none of the trajectories are corrupted (e.g. missing a temperature).
> ptrajProcessInputCoordinates(): Target replica temperature not found in
> traj! 100%
>
>
> PTRAJ: Successfully read in 589 sets and processed 589 sets.
>
> Dumping accumulated results (if any)
>
>
> Does any one know why?
>
> Thanks a lot,
>
> Nawel
>
>
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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 Fri Jul 04 2014 - 11:30:03 PDT
