On Tue, Jul 18, 2017 at 4:07 AM, Szymon Żaczek <szymonzaczek.gmail.com> wrote:
> Dear Dr Case,
I think you may have me confused with a far more accomplished scientist :-)
-Dan
>
> 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.
>
> 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
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Received on Tue Jul 18 2017 - 07:30:05 PDT
