From: Adrita Chakraborty (chakrabortyadrita652_at_gmail.com)
Date: Thu Apr 21 2022 - 08:54:13 CDT
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!rJD30Ow3lM8kKSjJqZZvgpRr1Wqs1uqXUx6dPgubcOG01DfoQiTuo-b8E4Er1jixjg$ >
>> )
>> 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!rJD30Ow3lM8kKSjJqZZvgpRr1Wqs1uqXUx6dPgubcOG01DfoQiTuo-b8E4Er1jixjg$ >
>> 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!rJD30Ow3lM8kKSjJqZZvgpRr1Wqs1uqXUx6dPgubcOG01DfoQiTuo-b8E4Er1jixjg$ >
>>
>> 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!rJD30Ow3lM8kKSjJqZZvgpRr1Wqs1uqXUx6dPgubcOG01DfoQiTuo-b8E4Eaej8QsQ$ >.
>>>>>
>>>>> 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
>
This archive was generated by hypermail 2.1.6 : Tue Dec 13 2022 - 14:32:44 CST