Re: [OpenGrowth] OpenGrowth issues (?)

[Nicolas C. <nic...@gm...>]

Hi,

1. I recommend you to use OpenBabel 2.4.1 for several reasons: (1) SMoG2016
was prepared with it (some atom types will be different with the two
versions of OpenBabel ; if someone wants to use OB 2.3.2, the
knowledge-based potential needs to be trained again), (2) it is faster in
some tasks, for example the 3mer screen. OpenGrowth does not use any of the
executables, it only needs the library.

2. The "ERROR: Could not set up force field" message is coming from
OpenBabel. It is discussed page 15 of the manual: " When the first chosen
fragment is a halide, you will very likely see “ERROR: Could not
setup force field”, the growth of this fragment will stop and a new growth
will start. This can be ignored. To avoid it, you can edit the file
Proba_FirstFrag.dat file and put 0.00000 at the lines defining halides.
This only impacts the choice of the first fragment, not the transition
probabilities so it won’t change anything to the molecules properties. This
disappears when halides are chosen later in the growth and not as the first
fragment. To know which fragments are what, you can look at the xyz files.
On the second line, you can find the name of the fragments, for example:
Ring0_2_1=fluorine, Ring0_7_1=chlorine, Ring0_10_1=bromine,
Ring0_11_1=iodine. When the first chosen fragment is hydroxyl, you may see
the following: “WARNING: damped steplength”. This can be safely ignored
since it is only a warning from OpenBabel." Did you change the halide lines
in Proba_FirstFrag.dat? If Yes and you still have that message, can you
please check if the first fragment is always the same in the grown
molecules?

3. I have never seen something like that (unconnected fragments). Are they
far from each other? Did you visually check them with different softwares
(could it be due to the criteria to draw a bond with your visualization
software)? If the problem is not coming from the visualization software,
can you please send me all your input files so I can try to reproduce the
problem?

4. Clashes should not happen. Something is going wrong. Which scoring
function are you using? In SMoG2016, there is a 1/r^12 term that prevents
this. In SMoG2001 there is a hard-wall potential that can be tuned in the
parameters (VDW_SCALE_INTER and VDW_SCAME_INTRA). If there was no problem
during the compilation of OpenBabel and OpenGrowth, you can send me your
input files so I can try here.

Nicolas




Le lun. 2 juil. 2018 à 14:08, ABRUSAN Gyorgy <Gyo...@ig...>
a écrit :

> Hi Nicolas,
>
>
> Just one correction, apparently my 2.4.1 OpenBabel wasn't installed (just
> compiled locally and tested), thats one of the causes of the different file
> structure, after recompiling and reinstalling it, and recompiling
> opengrowth with it nothing changes,  I still get the fragmented de novo
> ligands.
>
>
> Gyorgy
> ------------------------------
> *From:* ABRUSAN Gyorgy <Gyo...@ig...>
> *Sent:* 02 July 2018 10:40:40
> *To:* ope...@li...
> *Subject:* [OpenGrowth] OpenGrowth issues (?)
>
>
> Hi Nicolas,
>
> I ran a few tests with OG, and I have a few questions, also I think I
> found a few issues, that might be bugs. I describe them below.
>
>
> 1.Iinstallation of OpenBabel. I have both 2.3.2 and 2.4.1 installed
> (locally), and complied OG with both versions, but right now I symlink only
> the 2.3.2 executables in my home dir. Does OG use any of the OB
> executables, or just the headers and shared objects? (Also, my 2.4.1
> installation has a different file structure than 2.3.2, there is no
> openbabel-2.0 directory, the babelconfig.h header is located elsewhere than
> the other headers, etc.; but once the correct paths are provided OG
> compiles without issues.)
>
>
> 2.I frequently get the "ERROR: Could not set up force field" error
> message. Is it possible to fix this somehow? (their frequency varies, about
> 10% of the ligands seem to produce this).
>
>
> 3. Some of the ligands (*.xyz files) of OG (10-20%) contain unconnected
> fragments (Even when I use your test protein, 2aqu). The OG compiled with
> the OB 2.4.1. libraries appear to perform considerably worse in this
> respect, but it happens also with the version complied with OB 2.3.2. Their
> smiles seem to be okay though.
>
>
> 4.When I use a different test protein (5t8g), with a relatively small and
> deeply buried binding pocket, some of the grown ligands clash with the
> protein, sometimes (although rarely) entire sidechains are grown "into" the
> protein. Are there parameter combinations that may prevent this?
>
>
> Best wishes,
>
> Gyorgy
>
>
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