Hi Szymon,
>> thank you very much for your assistance, the fix obviously worked. I'd
>> suggest revising MCPB.py tutorial though to include the tip you gave
>> me.
>>
Thanks for your suggestion. I have added “restart” in the input file and submitted the change to the AMBER web git tree. It will appear online later sometime.
Kind regards,
Pengfei
>> Kind regards,
>> Szymon Żaczek
>>
>> 2017-07-18 1:09 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
>>> 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
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>
>
>
> --
> -------------------------
> 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 <https://www.lobos.nih.gov/lcb>
>
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Received on Thu Jul 27 2017 - 13:00:02 PDT
