Dear Dr Case,
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
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Received on Tue Jul 18 2017 - 01:30:03 PDT
