Dear Elvis,
I installed Miniconda3-latest-Linux-x86_64.sh which was not done earlier.
After installation in the bin folder of Miniconda3, I find conda instead of
amber.conda. So tried installing in the following way.
conda install -c anaconda numpy
I got following error message. How should I short it out?
I need your help.
Sincerely,
Sunita
------
conda install -c anaconda numpy
Collecting package metadata (current_repodata.json): failed
CondaHTTPError: HTTP 000 CONNECTION FAILED for url <
https://conda.anaconda.org/anaconda/linux-64/current_repodata.json>
Elapsed: -
An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your
way.
ConnectTimeout(MaxRetryError("HTTPSConnectionPool(host='conda.anaconda.org',
port=443): Max retries exceeded with url:
/anaconda/linux-64/current_repodata.json (Caused by
ConnectTimeoutError(<urllib3.connection.VerifiedHTTPSConnection object at
0x2ad7542504e0>, 'Connection to conda.anaconda.org timed out. (connect
timeout=9.15)'))"))
-------
conda install -c omnia openmm
Collecting package metadata (current_repodata.json): failed
CondaHTTPError: HTTP 000 CONNECTION FAILED for url <
https://conda.anaconda.org/omnia/linux-64/current_repodata.json>
Elapsed: -
--------
On Tue, Sep 24, 2019 at 5:28 PM Elvis Martis <elvis_bcp.elvismartis.in>
wrote:
> Best Regards
>
>
>
> On Tue, 24 Sep 2019 at 17:21, Sunita Patel <sunita.patel.cbs.ac.in> wrote:
>
> > Just after doing source amber.sh we ran 'parmed AH_ff14SB_CMAP.prmtop'
> and
> > got
> > No module named 'simtk'
> > No module named 'numpy'
> > Just install it using
>
> amber.conda install -c anaconda numpy >> this should solve the missing
> numpy
> amber.conda install -c omnia openmm >> this should solve the missing simtk
> problem
> Hope this helps.
>
>
>
>
>
> > Thanks for your help.
> > Sunita
> >
> >
> > On Tue, Sep 24, 2019 at 5:13 PM Elvis Martis <elvis_bcp.elvismartis.in>
> > wrote:
> >
> > > Just source the $AMNERHOME/amber.sh before typing parmed.
> > > Best Regards
> > >
> > >
> > >
> > > On Tue, 24 Sep 2019 at 16:58, Sunita Patel <sunita.patel.cbs.ac.in>
> > wrote:
> > >
> > > > Dear Elvis,
> > > >
> > > > When we checked 'parmed AH_leap_struct_CMAP.prmtop' following errors
> > > > appeared.
> > > >
> > > > ModuleNotFoundError: No module named 'simtk'
> > > > ModuleNotFoundError: No module named 'numpy'
> > > >
> > > > Looks like some of the modules are missing in my Amber18.
> > > > Pls suggest how to rectify it.
> > > >
> > > > Thanks for your help.
> > > >
> > > > Sincerely,
> > > > Sunita
> > > >
> > > >
> > > >
> > > > On Thu, Sep 19, 2019 at 5:12 PM Elvis Martis <
> elvis_bcp.elvismartis.in
> > >
> > > > wrote:
> > > >
> > > > > hello
> > > > > you would want to check the validity of the new prmtop file after
> > > adding
> > > > > CMAP parameters using parmed,
> > > > > See the following commands
> > > > > source $AMBERHOME/amber.sh
> > > > > parmed AH_leap_struct_CMAP.prmtop
> > > > > checkValidity
> > > > >
> > > > > If the prmtop file is corrupted while adding CMAP parameters parmed
> > > will
> > > > > tell.
> > > > >
> > > > > Best Regards
> > > > >
> > > > >
> > > > >
> > > > > On Thu, 19 Sep 2019 at 17:01, Sunita Patel <sunita.patel.cbs.ac.in
> >
> > > > wrote:
> > > > >
> > > > > > Dear Users,
> > > > > >
> > > > > > We are trying to convert *.prmtop and *.rst files obtained after
> > > energy
> > > > > > minimization into a pdb file using ambpdb command. The *.prmtop
> > file
> > > is
> > > > > > obtained by adding extra CMAP parameters (FF14IDPSFF) to the
> > > original
> > > > > > prmtop file obtained from FF14SB force field. However, we got the
> > > > > following
> > > > > > error message.
> > > > > >
> > > > > > ambpdb -p AH_leap_struct_CMAP.prmtop -c AH_struct_min.rst >
> > > > > > AH_struct_min.pdb
> > > > > > Segmentation fault (core dumped)
> > > > > >
> > > > > > When we are converting the prmtop file to pdb without adding CMAP
> > > > > > parameters, we could successfully do that without any error.
> > > > > > How can we get the pdb file by using the prmtop file with the
> CMAP
> > > > > > parameters?
> > > > > >
> > > > > > Sincerely,
> > > > > > Sunita
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 25 2019 - 01:30:02 PDT
