Change 'fixed.metal_solv.inpcrd' to 'fixed.metal_solv.rst7' or add
'restart' keyword to 'trajout'. If you check your cpptraj output you'll see
that .inpcrd is not a recognized extension so cpptraj defaults to Amber
trajectory. See the manual for full details of recognized extensions and
keywords for 'trajout'.
-Dan
On Mon, Jul 17, 2017 at 2:54 PM Szymon Żaczek <szymonzaczek.gmail.com>
wrote:
> Dear Amber developers,
>
> I am creating metal parameters for Mn using bonded model strictly
> following tutorial
> (http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm).
> Everything has gone pretty fine, up until the very end, when an error
> occurred when I tried to load my topology and coordinates into
> cpptraj. The error is the same as it was specified in tutorial:
>
> Error: Atom 7908 was assigned a lower molecule # than previous atom.
> Error: This can happen if bond information is incorrect or missing, or
> if the
> Error: atom numbering in molecules is not sequential. Try one of the
> Error: following:
> Error: - If this is a PDB file, try using the 'noconect' keyword.
> Error: - If this topology did not have bond info, try increasing the bond
> Error: search cutoff above 0.2 Ang. ('bondsearch <cutoff>').
> Error: - Use the 'fixatomorder' command to reorder the topology and any
> Error: associated coordinates.
> Error: - Use the 'setMolecules' command in parmed to reorder only the
> Error: topology.
> Error: Could not determine molecule information for metal_solv.prmtop.
> Error: SetSolventInfo: No molecule information.
> Error: Could not determine solvent information for metal_solv.prmtop.
>
> I followed the advices about fixing atom order given in tutorial and
> http://archive.ambermd.org/201507/0402.html. This is my script for
> fixing atom order:
>
> fixatomorder outprefix fixed
> trajin metal_solv.inpcrd
> trajout fixed.metal_solv.inpcrd
> run
> quit
>
> I run this script using command:
>
> cpptraj -p metal_solv.prmtop -i fixatord.in > fixatord.out
>
> The output file is as follows:
>
> Reading 'metal_solv.prmtop' as Amber Topology
> INPUT: Reading input from 'fixatord.in'
> [fixatomorder outprefix fixed]
> Warning: Action specified before trajin/ensemble. Assuming trajin.
> FIXATOMORDER: Will attempt to fix atom ordering when atom numbering
> in molecules is non-sequential.
> Re-ordered topology will be output with prefix fixed
> [trajin metal_solv.inpcrd]
> Reading 'metal_solv.inpcrd' as Amber Restart
> [trajout fixed.metal_solv.inpcrd]
> Warning: Format not specified and extension '.inpcrd' not recognized.
> Defaulting to Amber Trajectory.
> Writing 'fixed.metal_solv.inpcrd' as Amber Trajectory
> [run]
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES (1 total):
> 0: metal_solv.prmtop, 64277 atoms, 19310 res, box: Orthogonal, 0 mol
>
> INPUT TRAJECTORIES (1 total):
> 0: 'metal_solv.inpcrd' is an AMBER restart file, no velocities, Parm
> metal_solv.prmtop (Orthogonal box) (reading 1 of 1)
> Coordinate processing will occur on 1 frames.
>
> OUTPUT TRAJECTORIES (1 total):
> 'fixed.metal_solv.inpcrd' (1 frames) is an AMBER trajectory
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM 'metal_solv.prmtop' (1 actions):
> 0: [fixatomorder outprefix fixed]
> Detected 18799 molecules.
> Re-ordered parm: 64277 atoms, 19310 res, box: Orthogonal,
> 18799 mol, 18783 solvent
> Writing topology 0 (metal_solv.prmtop) to
> 'fixed.metal_solv.prmtop' with format Amber Topology
> ----- metal_solv.inpcrd (1-1, 1) -----
> 100% Complete.
>
> Read 1 frames and processed 1 frames.
> TIME: Avg. throughput= 2.6128 frames / second.
>
> ACTION OUTPUT:
>
> RUN TIMING:
> TIME: Init : 0.0000 s ( 0.00%)
> TIME: Trajectory Process : 0.3827 s ( 97.59%)
> TIME: Action Post : 0.0000 s ( 0.00%)
> TIME: Analysis : 0.0000 s ( 0.00%)
> TIME: Data File Write : 0.0000 s ( 0.00%)
> TIME: Other : 0.0094 s ( 0.02%)
> TIME: Run Total 0.3922 s
> ---------- RUN END ---------------------------------------------------
>
> The problem is, however, when I want to start running simulations,
> beginning from minimization job, in the output following error is to
> be found:
>
> | ERROR: Could not read second line of fixed.metal_solv.inpcrd
> | Bad inpcrd file!
>
>
> First three lines of my fixed.metal_solv.inpcrd:
>
> Cpptraj Generated trajectory
> 73.599 53.001 21.001 74.334 53.652 21.189 73.931 52.285 20.388
> 72.828
> 53.476 20.578 73.156 52.387 22.271 73.925 52.466 22.923 71.935
> 53.136
>
>
> It seems to me as if Amber treats my fixed.metal_solv.inpcrd file as
> it was trajectory instead of rst file, as it was also stated in
> cpptraj output. Do you have any idea how can I prepare coordinate file
> properly so there are no issues with numbering and the file could be a
> starting point for following simulations?
>
> Kind regards,
> Szymon Zaczek
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Jul 17 2017 - 16:30:03 PDT
