From: Hrishikesh Dhondge (hbdhondge_at_gmail.com)
Date: Tue Apr 26 2022 - 10:19:33 CDT
Hello,
Sorry for the late reply. Have you tried installing ambertools?
ambertools might be required for cpptraj in some cases.
I hope it helps.
On Thu, Apr 21, 2022 at 3:54 PM Adrita Chakraborty <
chakrabortyadrita652_at_gmail.com> wrote:
> Yes I did the very same. But I am facing the following error:
>
>
>
> Collecting package metadata (current_repodata.json): done
> Solving environment: /
> The environment is inconsistent, please check the package plan carefully
> The following packages are causing the inconsistency:
>
> - <unknown>/linux-64::cpptraj==2016.0.07=0
> failed with initial frozen solve. Retrying with flexible solve.
> Solving environment: failed with repodata from current_repodata.json, will
> retry with next repodata source.
> Collecting package metadata (repodata.json): done
> Solving environment: \
> The environment is inconsistent, please check the package plan carefully
> The following packages are causing the inconsistency:
>
> - <unknown>/linux-64::cpptraj==2016.0.07=0
> failed with initial frozen solve. Retrying with flexible solve.
> Solving environment: \
> Found conflicts! Looking for incompatible packages.
> This can take several minutes. Press CTRL-C to abort.
> failed
>
> UnsatisfiableError: The following specifications were found to be
> incompatible with each other:
>
> Output in format: Requested package -> Available versions
>
> Package vs2015_runtime conflicts for:
> python=3.9 -> vc[version='>=14.1,<15.0a0'] ->
> vs2015_runtime[version='>=14.15.26706|>=14.27.29016|>=14.16.27012']
> python=3.9 -> vs2015_runtime[version='>=14.16.27012,<15.0a0']
> cpptraj -> libnetcdf -> vs2015_runtime[version='>=14.16.27012,<15.0a0']
>
>
> Regards
> Adrita Chakraborty
>
> On Thu, Apr 21, 2022 at 4:39 PM Hrishikesh Dhondge <hbdhondge_at_gmail.com>
> wrote:
>
>> Hello,
>>
>> If you are installing through conda, you don't have to download
>> anything prior. Just select any conda environment you want to work with and
>> use the following command:
>>
>> conda install -c omnia cpptraj
>>
>>
>> On Thu, Apr 21, 2022 at 11:18 AM Adrita Chakraborty <
>> chakrabortyadrita652_at_gmail.com> wrote:
>>
>>> Yes, I tried it both on windows and linux. But I am facing an error
>>> during the installation.
>>> These are the steps which I followed:
>>> 1) I did download the file ( linux-64/cpptraj-2016.0.07-0.tar.bz2
>>> <https://urldefense.com/v3/__https://anaconda.org/omnia/cpptraj/2016.0.07/download/linux-64/cpptraj-2016.0.07-0.tar.bz2__;!!DZ3fjg!9kXz_YnxOV4XNbB_nOaJA75qmlCU4OcovPyOHq_RobAN0JsAg3uSnvo_QGQF_VOprScAhthEQeVCHIIFwpU$ >
>>> )
>>> 2) these are the commands I used to install
>>>
>>> anaconda upload linux-64/cpptraj-2016.0.07-0.tar.bz2
>>> <https://urldefense.com/v3/__https://anaconda.org/omnia/cpptraj/2016.0.07/download/linux-64/cpptraj-2016.0.07-0.tar.bz2__;!!DZ3fjg!9kXz_YnxOV4XNbB_nOaJA75qmlCU4OcovPyOHq_RobAN0JsAg3uSnvo_QGQF_VOprScAhthEQeVCHIIFwpU$ >
>>> conda install -c omnia cpptraj-2016.0.07-0.tar.bz2
>>> <https://urldefense.com/v3/__https://anaconda.org/omnia/cpptraj/2016.0.07/download/linux-64/cpptraj-2016.0.07-0.tar.bz2__;!!DZ3fjg!9kXz_YnxOV4XNbB_nOaJA75qmlCU4OcovPyOHq_RobAN0JsAg3uSnvo_QGQF_VOprScAhthEQeVCHIIFwpU$ >
>>>
>>> After extraction, a folder named "cpptraj" is also created.
>>> But then after this, when I am trying to run the following command i.e.
>>>
>>> cpptraj nativecontacts name prot :1-39 :87-174 distance 5.0
>>> noimage byresidue writecontacts trial_interprot.dat
>>>
>>> This is the error I am facing:
>>> error while loading shared libraries libopenblas.so. cannot open shared
>>> object file
>>> No such file or directory cpptraj error while loading shared libraries
>>> libopenblas.so cannot open shared object file
>>> No+such file or directory&aqs=chrome
>>>
>>>
>>>
>>>
>>> On Thu, Apr 21, 2022 at 12:43 PM Hrishikesh Dhondge <hbdhondge_at_gmail.com>
>>> wrote:
>>>
>>>> Hello Adrita,
>>>>
>>>> You can use CPPTRAJ independently from AMBER. As you mentioned, it can
>>>> be installed from conda.
>>>>
>>>> I hope it helps.
>>>>
>>>> On Thu, 21 Apr 2022, 08:45 Adrita Chakraborty, <
>>>> chakrabortyadrita652_at_gmail.com> wrote:
>>>>
>>>>> Hello Hrishikesh
>>>>>
>>>>> Thank You so much for your response.
>>>>>
>>>>> I had a small query, sorry to bother you. In order to use cpptraj, do
>>>>> we need to install amber or can we independently work with cpptraj
>>>>> (provided pip / conda is installed)?
>>>>>
>>>>> Thanking you in advance
>>>>>
>>>>> Regards
>>>>> Adrita Chakraborty
>>>>>
>>>>> On Wed, Apr 20, 2022 at 11:38 AM Hrishikesh Dhondge <
>>>>> hbdhondge_at_gmail.com> wrote:
>>>>>
>>>>>> Hello Adrita,
>>>>>>
>>>>>> You can get the interprotein contacts using nativecontacts command
>>>>>> from CPPTRAJ. The command will be as follows:
>>>>>>
>>>>>> nativecontacts name prot :molA_range :molB_range distance 5.0 noimage
>>>>>>> byresidue writecontacts frame_native_contact.dat
>>>>>>
>>>>>>
>>>>>> you can specify the same range, for example, your protein is of 10
>>>>>> residues from 1-10 then as follows:
>>>>>>
>>>>>>> nativecontacts name prot :1-10 :1-10 distance 5.0 noimage byresidue
>>>>>>> writecontacts trial_interprot.dat
>>>>>>
>>>>>>
>>>>>> More information on this can be found here
>>>>>> <https://urldefense.com/v3/__https://amberhub.chpc.utah.edu/nativecontacts/__;!!DZ3fjg!9kXz_YnxOV4XNbB_nOaJA75qmlCU4OcovPyOHq_RobAN0JsAg3uSnvo_QGQF_VOprScAhthEQeVCSktf4dM$ >.
>>>>>>
>>>>>> On Tue, Apr 19, 2022 at 4:15 PM Adrita Chakraborty <
>>>>>> chakrabortyadrita652_at_gmail.com> wrote:
>>>>>>
>>>>>>> Dear NAMD users'
>>>>>>>
>>>>>>> I want to calculate the inter contacts between two proteins from the
>>>>>>> psf and dcd (trajectory) files.
>>>>>>> Can someone suggest to me how to go about this?
>>>>>>>
>>>>>>>
>>>>>>> Best Regards
>>>>>>> Adrita Chakraborty
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> With regards
>>>>>> Hrishikesh Dhondge
>>>>>> PhD student,
>>>>>> LORIA - INRIA Nancy
>>>>>>
>>>>>
>>
>> --
>> With regards
>> Hrishikesh Dhondge
>> PhD student,
>> LORIA - INRIA Nancy
>>
>
-- With regards Hrishikesh Dhondge PhD student, LORIA - INRIA Nancy
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