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GAFF2 in babel?

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GAFF2 in babel?

Albert
Hello:

I noticed that GAFF2 is released in recent Amber 16. I am just wondering
how can we implement it to openBabel?

Than you very much

Albert

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Re: GAFF2 in babel?

David Hall
Is there documentation beyond the Amber source code? Do you know if the difference is just using gaff2.dat instead of gaff.dat?



On Wed, Jul 13, 2016 at 4:58 PM, Albert <[hidden email]> wrote:
Hello:

I noticed that GAFF2 is released in recent Amber 16. I am just wondering
how can we implement it to openBabel?

Than you very much

Albert

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Re: GAFF2 in babel?

David Hall
poking around, it appears there are some new atom types in dat/antechamber/ATOMTYPE_GFF2.DEF . Since AmberTools is GPLv3, I'll leave it to others to decide what that means for the ability to implement gaff2 . I'll note that gaff2.dat is public domain though, so that part should be clean.

On Thu, Jul 14, 2016 at 9:54 AM, David Hall <[hidden email]> wrote:
Is there documentation beyond the Amber source code? Do you know if the difference is just using gaff2.dat instead of gaff.dat?



On Wed, Jul 13, 2016 at 4:58 PM, Albert <[hidden email]> wrote:
Hello:

I noticed that GAFF2 is released in recent Amber 16. I am just wondering
how can we implement it to openBabel?

Than you very much

Albert

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Re: GAFF2 in babel?

Albert
In reply to this post by Albert


I found the following difference between Gaff 1.x and GAFF 2:

1. All the sp2 carbon in a AR2 ring (such as pyrrole, furan, pyrazole)
are either ’cc’ or ’cd’ atom types (not
’c2’ any more). This is suggested by Gabriel Rocklin from UCSF. This
modification improves the planarity
of multiple-ring systems

2. New van der Waals parameters have been developed for ’br’ and ’i’
atom types. The current parameters can
well reproduce the experimental density data of CH3 Br (1.6755, 20
degree) and CH3 I (2.2789, 20 degree):
1.642 for CH3 Br and 2.25 for CH3 I, in contrast, the old parameters
give 1.31 and 1.84, respectively.[325]

3. New van der Waals parameters have been suggested by David Mobley for
’c1’, ’cg’ and ’ch’ atom types.[326]

4. We have performed B3LYP/6-31G* optimization for 15 thousands marketed
or experimental drugs/bio-
actives. Reliable bond length and bond angle equilibrium parameters were
obtained by statistics: each bond
length parameter must show up at least five times and has a rmsd smaller
than 0.02 Å; each bond angle
parameter must show up at least five times and has a rmsd smaller than
2.5 degrees. Those new parameters
not showing up in old gaff were directly added into gaff 1.4; and some
low-quality gaff parameters which
show up less than five times or have large rmsd values (>0.02 Å for bond
length and >5 degrees for bond
angles) were replaced with those newly generated. In summary, 59 low
quality bond stretching parameters
were replaced and 56 new parameters were introduced; 437 low quality
bond bending parameters were
replaced and 618 new parameters were introduced.


I don't know whether people would like to implement this new GAFF2 into
BABEL...............


On 07/14/2016 03:54 PM, David Hall wrote:
> Is there documentation beyond the Amber source code? Do you know if
> the difference is just using gaff2.dat instead of gaff.dat?




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Re: GAFF2 in babel?

David van der Spoel
On 15/07/16 14:12, Albert wrote:

>
>
> I found the following difference between Gaff 1.x and GAFF 2:
>
> 1. All the sp2 carbon in a AR2 ring (such as pyrrole, furan, pyrazole)
> are either ’cc’ or ’cd’ atom types (not
> ’c2’ any more). This is suggested by Gabriel Rocklin from UCSF. This
> modification improves the planarity
> of multiple-ring systems
>
> 2. New van der Waals parameters have been developed for ’br’ and ’i’
> atom types. The current parameters can
> well reproduce the experimental density data of CH3 Br (1.6755, 20
> degree) and CH3 I (2.2789, 20 degree):
> 1.642 for CH3 Br and 2.25 for CH3 I, in contrast, the old parameters
> give 1.31 and 1.84, respectively.[325]
>
> 3. New van der Waals parameters have been suggested by David Mobley for
> ’c1’, ’cg’ and ’ch’ atom types.[326]
>
> 4. We have performed B3LYP/6-31G* optimization for 15 thousands marketed
> or experimental drugs/bio-
> actives. Reliable bond length and bond angle equilibrium parameters were
> obtained by statistics: each bond
> length parameter must show up at least five times and has a rmsd smaller
> than 0.02 Å; each bond angle
> parameter must show up at least five times and has a rmsd smaller than
> 2.5 degrees. Those new parameters
> not showing up in old gaff were directly added into gaff 1.4; and some
> low-quality gaff parameters which
> show up less than five times or have large rmsd values (>0.02 Å for bond
> length and >5 degrees for bond
> angles) were replaced with those newly generated. In summary, 59 low
> quality bond stretching parameters
> were replaced and 56 new parameters were introduced; 437 low quality
> bond bending parameters were
> replaced and 618 new parameters were introduced.
>
>
> I don't know whether people would like to implement this new GAFF2 into
> BABEL...............
>
Yes, BUT! What Babel version are you using? We have recently implemented
an updated gaff.prm in OB (if you download the git version you will find
it). It was very difficult to get everything close to perfect. We
compared the assignments due to Antechamber and OB, and tried to fix OB
as good as we could. However Antechamber had errors as well (compared to
the Wang2005 paper).

So there are TWO issues, first the force field parameters, and second
the atom typing. Both should be treated in one go.


>
> On 07/14/2016 03:54 PM, David Hall wrote:
>> Is there documentation beyond the Amber source code? Do you know if
>> the difference is just using gaff2.dat instead of gaff.dat?
>
>
>
>
> ------------------------------------------------------------------------------
> What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
> patterns at an interface-level. Reveals which users, apps, and protocols are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity planning
> reports.http://sdm.link/zohodev2dev
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[hidden email]    http://folding.bmc.uu.se

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Re: GAFF2 in babel?

Geoff Hutchison
In reply to this post by Albert
> I don't know whether people would like to implement this new GAFF2 into
> BABEL...............

Sure, although as David van der Spoel mentioned, there was a considerable effort in updating the parameters and typing recently.

Personally, I'd push to see if the GAFF2 developers can set up a test/validation set, much like MMFF94. That had a set of ~700-800 molecules with assigned types and validated energies.

If there were a validation set (and ideally a publication) it would be much easier to ensure reliable implementations in Open Babel (or RDKit or ..)

Who would be a good contact person?

Cheers,
-Geoff
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