From: Adrita Chakraborty (chakrabortyadrita652_at_gmail.com)
Date: Thu Apr 21 2022 - 04:18:05 CDT
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!oStPkuAgFKy0tNAbU0IwRxYFhJrMsJGnGjdMlquMl6sDZLon-AIzGJ5TcPduWX0RJQ$ >
)
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!oStPkuAgFKy0tNAbU0IwRxYFhJrMsJGnGjdMlquMl6sDZLon-AIzGJ5TcPduWX0RJQ$ >
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!oStPkuAgFKy0tNAbU0IwRxYFhJrMsJGnGjdMlquMl6sDZLon-AIzGJ5TcPduWX0RJQ$ >
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!oStPkuAgFKy0tNAbU0IwRxYFhJrMsJGnGjdMlquMl6sDZLon-AIzGJ5TcPf1CMvwWw$ >.
>>>
>>> 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
>>>
>>
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