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zhenglz / dockingML

A package for MD, Docking and Machine learning drug discovery pipeline
GNU General Public License v3.0
40 stars 22 forks source link

repository does not exist #5

Open lalehan opened 5 years ago

lalehan commented 5 years ago

Hello, I'm trying to install through git and this error occurs: fatal: repository 'zhenglz@github.com/zheng/dockingML.git' does not exist

Could you please provide some guidance? Thanks.

zhenglz commented 5 years ago

Hello, I'm trying to install through git and this error occurs: fatal: repository 'zhenglz@github.com/zheng/dockingML.git' does not exist

Could you please provide some guidance? Thanks.

There is an error in the README.md file. Now the bug has been fixed. The right way to install the package is:

$ cd /home/john/applications $ pip install networkx $ pip install mdtraj $ git clone https://github.com/zhenglz/dockingML.git $ cd dockingML $ pip install ./ Or you may use Anaconda to install the package. Please refer to the README page. $ conda create -name mdanaly python=3.6 $ source activate mdanaly $ conda install -c omnia mdtraj $ conda install pandas mpi4py numpy matplotlib sklearn networkx $ conda install -c rdkit rdkit $ cd $HOME/applications/dockingML $ pip install .

lalehan commented 5 years ago

Thank you for the guidance, it actually worked. No problem with installation anymore, however when I run gmx_cmap.py, the error in the picture occurs. cmap_error

zhenglz commented 5 years ago

Thank you for the guidance, it actually worked. No problem with installation anymore, however when I run gmx_cmap.py, the error in the picture occurs. cmap_error

I may suggest you have a python 3.5 or 3.6, then install the package. It would be preferred to set up the environment with anaconda.

lalehan commented 5 years ago

I did exactly the same and the error persists: error_in_py35 Does it have anything to do with the default python version on the system?

zhenglz commented 5 years ago

I did exactly the same and the error persists: error_in_py35 Does it have anything to do with the default python version on the system?

Note that although you are using Python 3.5, your python libraries are still 2.7. See the figure you provided.

A potential solution is unset pythonpath using: $ source deactive # to escape from py35 environment $ unset PYTHONPATH $ unset PYTHONHOME $ source activate py35 $ gmx_cmap.py -h

lalehan commented 5 years ago

Yes, that's what I thought. I wanted to make Python 3 default for that matter, but couldn't do it yet. I tried your solution: setpy

zhenglz commented 5 years ago

Quite strange.

You may now try these:

under py35

$ source activate py35 $ cd dockingML $ which pip # make sure that pip is in xx/envs/py35/bin/pip $ pip install ./ # try to install the package again $ cd xx/dockingML/bin $ python ./gmx_cmap.py -h

lalehan commented 5 years ago

I think I'll try yum install Glibc 2.14 now and see what happens: glib

zhenglz commented 5 years ago

The package now is working as desired. But seems some library is not compatible with mdtraj.

Yes, Glibc 2.14 may need to be upgraded. You may find this link useful: https://unix.stackexchange.com/questions/176489/how-to-update-glibc-to-2-14-in-centos-6-5

lalehan commented 5 years ago

I was just reading that :) Thank you very much, really. This was way more than helpful. I'll post here once I manage to run. Best,

zhenglz commented 5 years ago

I was just reading that :) Thank you very much, really. This was way more than helpful. I'll post here once I manage to run. Best,

No problem.

lalehan commented 5 years ago

Looks like my errors get better: coredum I feel I'm getting somewhat closer. Thanks again!

zhenglz commented 5 years ago

ps_01 I have never seen such an error. "core dumped" may be caused by a lot of different reasons. I am not sure how to deal with this error.

But you could try the code in python console and return me your output: $ python

from mdanaly import cmap import dockml

lalehan commented 5 years ago

Here it is: python

zhenglz commented 5 years ago

Ah, confused.

What about:

python

import mdtraj as mt import numpy as np

lalehan commented 5 years ago

Here: np

zhenglz commented 5 years ago

Then it seems like that mdtraj is not well installed. The error may raise from the glibc. You may need to re-install glibc after you upgrade your centos. And reinstall mdtraj and the package again.

lalehan commented 5 years ago

Thank you again so much. I guess I really should upgrade centos which seems tricky (this workstation is open to common use). However that looks like the only way to get away with it. Later I will reinstall mdtraj and the package again. Many thanks, once I manage I'll post it here :)

zhenglz commented 5 years ago

Glad to be helpful!

lalehan commented 5 years ago

Hello again, I switched to a newer Centos and it works :) Thank you again! I run gmx_cmap.py, but it requests: xyz I have no idea when I supplied 1000, 130643, 1. If this is an issue to solve by further reading, please guide me. I couldn't locate it anywhere.

zhenglz commented 5 years ago

Hello again, I switched to a newer Centos and it works :) Thank you again! I run gmx_cmap.py, but it requests: xyz I have no idea when I supplied 1000, 130643, 1. If this is an issue to solve by further reading, please guide me. I couldn't locate it anywhere.

The error comes from the inconsistancy of atom numbers in your xtc and referece pdb file.

Mdtraj loads the xtc file using a mdtraj.iterload() method, which requires a xtc file and a reference pdb file as inputs. The reference pdb works as the topology, the same function as the -s md.tpr in trjconv in Gromacs. Please make sure that the number of atoms in xtc file is the same as the reference pdb.

For example, for your system, you may have 12305 non-water molecules/ions atoms. So make sure both the xtc and reference pdb (specified through gmx_cmap.py -s reference.pdb) has the same number of atoms. You may process the xtc file and reference.pdb file using gmx trjconv before performing contact map calculation.

lalehan commented 5 years ago

Thank you very much, I think it will be pretty straightforward by trjconv command. All the best,

lalehan commented 5 years ago

Hello again, I managed to run gmx_cmap.py. Thank you for everything. However, I'm not sure if it's really useful for obtaining a contact map between ligand and protein. I'm doing this: screenshot from 2019-01-31 17-34-54 Is this only applicable for protein-protein contacts? Many thanks, best regards..

zhenglz commented 5 years ago

You may use -at all all to generate a all-atom based contact map between the protein and a ligand.

lalehan notifications@github.com于2019年1月31日 周四下午10:37写道：

Hello again, I managed to run gmx_cmap.py. Thank you for everything. However, I'm not sure if it's really useful for obtaining a contact map between ligand and protein. I'm doing this: [image: screenshot from 2019-01-31 17-34-54] https://user-images.githubusercontent.com/41117553/52061140-b8520200-257e-11e9-87eb-bae2a8a5e54d.png Is this only applicable for protein-protein contacts? Many thanks, best regards..

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lalehan commented 5 years ago

Looks like it's working :) Thanks again :)