Re: [AMBER] .crd error

From: MYRIAN TORRES RICO <myriam.torres.iiq.csic.es>
Date: Tue, 04 Feb 2020 13:57:09 +0100

Hi Gustaf,

I checked using as output.rst7 but I obtained a lot of files (as a
descomposition of coordinates...), I have attached a picture with this.
I looking your table..I'm going to test with output.nc.

Thanx in advance


Myriam

Gustaf Olsson <gustaf.olsson.lnu.se> escribió:

> 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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>>
>>
>>
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rst7.jpg
(image/jpeg attachment: rst7.jpg)

Received on Tue Feb 04 2020 - 05:00:03 PST
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