search

forlilab / waterkit

Tool to predict water molecules placement and energy in ligand binding sites
GNU General Public License v3.0
26 stars 8 forks source link

Installation issues #1

Closed zhentg closed 1 year ago

zhentg commented 1 year ago

Dear developer

cd autogrid autoreconf -i mkdir x86_64Linux2 # for x86_64architecture cd x86_64Linux2 ../configure make

After the above commands, compilation of autogrid stops with error make: *** No rule to make target '../../autodock/paramdat2h.csh', needed by 'default_parameters.h'. Stop.

Could you help on this?

Zhenting

jeeberhardt commented 1 year ago

Hi @zhentg,

Sorry for the inconvenience, it looks like I didn't try compiling autogrid after putting it on GitHub. Unfortunately, I am traveling right now and don't have access to my workstation. I will come back to you as soon as possible (either with a temporary fix or a permanent one)!

MKCarter commented 1 year ago

You can void the need to use the source code foir autogrid by installing it via conda:

conda install -c bioconda autogrid

Should give you a working autogrid4 installation

jeeberhardt commented 1 year ago

Hi @MKCarter,

Nope, you can't. WaterKit uses a modified version of autogrid, with Amber FF atom types. The number of atom types is rather restricted to a limited number in the vanilla version of autogrid. This version expands the number to 56.

jeeberhardt commented 1 year ago

Hi @zhentg,

A new version is up, you can now compile autogrid4. Tell me if it works for you!

Best,

MKCarter commented 1 year ago

Hi @MKCarter,

Nope, you can't. WaterKit uses a modified version of autogrid, with Amber FF atom types. The number of atom types is rather restricted to a limited number in the vanilla version of autogrid. This version expands the number to 56.

Ah I see... thanks for letting me know. Your fresh install instructions, work for me also. Thanks

zhentg commented 1 year ago

Hi @jeeberhardt ,

Sorry for the late response. After downloading the latest code, I executed the following commands for compilation

cd autodocksuite-4.2.6-src/autogrid; autoreconf -i; mkdir x86_64Linux2 # for x86_64architecture; cd x86_64Linux2; ../configure; make; make install; #(optional)

I used a non-root account for the installation, and met the following errors. I think the default location of autogrid should be changed accordingly to solve it. How to?

make[1]: Leaving directory '/tools/solvation/waterkit-master/autodocksuite-4.2.6-src/autogrid/x86_64Linux2' make install-am make[1]: Entering directory '/tools/solvation/waterkit-master/autodocksuite-4.2.6-src/autogrid/x86_64Linux2' make[2]: Entering directory '/tools/solvation/waterkit-master/autodocksuite-4.2.6-src/autogrid/x86_64Linux2' /usr/bin/mkdir -p '/usr/local/bin' /usr/bin/install -c autogrid4 '/usr/local/bin' /usr/bin/install: cannot create regular file '/usr/local/bin/autogrid4': Permission denied make[2]: [Makefile:475: install-binPROGRAMS] Error 1 make[2]: Leaving directory '/tools/solvation/waterkit-master/autodocksuite-4.2.6-src/autogrid/x86_64Linux2' make[1]: [Makefile:1075: install-am] Error 2 make[1]: Leaving directory '/tools/solvation/waterkit-master/autodocksuite-4.2.6-src/autogrid/x86_64Linux2' make: *** [Makefile:1069: install] Error 2

zhentg commented 1 year ago

'make install' is optional. I skipped it and autogrid is compiled successfully.

zhentg commented 1 year ago

@jeeberhardt

While executing configure, there is a warning about the script 'missing', is it important?

checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes /tools/solvation/waterkit-master/autodocksuite-4.2.6-src/autogrid/missing: Unknown '--is-lightweight' option Try '/tools/solvation/waterkit-master/autodocksuite-4.2.6-src/autogrid/missing --help' for more information configure: WARNING: 'missing' script is too old or missing