The file format and autodetect function has got me stuck before, I have not checked recently though using an updated version of amber/ambertools NetCDF is the default format for trajectories and restart files. I made this table some time ago so I donated know how accurate it is:
Format Keyword(s) Extension Notes
Amber Trajectory crd .crd Default format if keywords/extensions not recognised
Aber NetCDF cdf,nedcdf .nc No compression
Amber Restart restart .rst7
Amber NetCDF Restart ncrestart, restartnc .ncrst
Charmm DCD dcd, charmm .dcd
Charmm COR cor .cor Read Only
PDB pdb .pdb
Mol2 mol2 .mol2
Scripts Binpos binpos .binpos
Gromacs TRR trr .trr
Gromacs GRO gro .gro Read Only
Gromacs XTC xtc .xtc
CIF cif .cif Read Only
Tinker ARC arc .arc Read Only
SQM Input sqm .sqm Write Only
SDF pdf .sdf Read Only
LMOD Conflib conflib .conflib Read Only, Detection by extension
If this is still correct, “.rst” might not be correctly interpreted, though it might be some completely other problem as well. From what I remember (without checking the manual) you can either specify the correct filetype extension
cpptraj -p [PRMTOP] -y [INPUT] -x [OUTPUT].rst7
Where -y is a trajectory as in your example (mdcrd) (otherwise -i I think). You can also specify the filetype/format to use though I don’t remember the syntax at the moment.
// Gustaf
> On 4 Feb 2020, at 10:12, MYRIAN TORRES RICO <myriam.torres.iiq.csic.es> wrote:
>
> Hi Daniel,
>
> I saw the manual and I have tested this script:
>
> parm smp-198-mdk0rig.top
> trajin smp-198mdk0rig_vcon3.mdcrd
> trajout smp-198mdk0rig_vcon3.rst
>
> but the file .rst still not work...any idea? .rst is a restart format, no?
>
>
> thanx in advance,
>
>
> Myriam
>
>
> Daniel Roe <daniel.r.roe.gmail.com> escribió:
>
>> Hi,
>>
>> The ".crd" extension for output trajectories means "Amber ASCII
>> trajectory" (you can verify this in the output from CPPTRAJ under
>> OUTPUT TRAJECTORIES ). Trajectories cannot be used to restart MD
>> simulations. You need to convert to a restart format (ASCII or
>> netcdf), either by using the appropriate keyword or extension (e.g.
>> .rst7): see the manual for full details.
>>
>> -Dan
>>
>> On Mon, Feb 3, 2020 at 4:16 AM MYRIAN TORRES RICO
>> <myriam.torres.iiq.csic.es> wrote:
>>>
>>>
>>> Hi,
>>>
>>> I have problem with my coordenates extension. I want to launch a short
>>> molecular dynamic with restrictions using the final coordenates, to
>>> correct the distorsions in my complexe.
>>> At first this error appeared:
>>>
>>> Could not read second line of ./leap/smp-198mdk0rig_vcon3.mdcrd
>>>
>>>
>>> So, I though to change the extension of this file to .crd. I created
>>> the next script:
>>>
>>> parm smp-198-mdk0rig.top
>>> trajin smp-198mdk0rig_vcon3.mdcrd
>>> trajout smp-198mdk0rig_vcon3.crd
>>> go
>>> exit
>>>
>>>
>>> The extension changed, but this error continues appearing...any idea?
>>>
>>>
>>>
>>> Thanx in advance,
>>>
>>>
>>> Myriam
>>>
>>>
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>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>
>
>
>
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Received on Tue Feb 04 2020 - 03:30:02 PST
