From: Hrishikesh Dhondge (hbdhondge_at_gmail.com)
Date: Thu Apr 21 2022 - 06:09:16 CDT
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!tZMBrS2M_OKs6bsTTnNBOvn0uDoO2SQwE7zz0wvLSMNXLW5MDTE8UEoXxelyFF1sbg$ >
> )
> 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!tZMBrS2M_OKs6bsTTnNBOvn0uDoO2SQwE7zz0wvLSMNXLW5MDTE8UEoXxelyFF1sbg$ >
> 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!tZMBrS2M_OKs6bsTTnNBOvn0uDoO2SQwE7zz0wvLSMNXLW5MDTE8UEoXxelyFF1sbg$ >
>
> 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!tZMBrS2M_OKs6bsTTnNBOvn0uDoO2SQwE7zz0wvLSMNXLW5MDTE8UEoXxekNAwS16Q$ >.
>>>>
>>>> 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
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