distorted rings with obminimize -ff GAFF

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distorted rings with obminimize -ff GAFF

Eiso AB-2
(installation: Open Babel 2.4.0)

I'm getting a distorted ring (the 5-ring) when using
obminimize with -ff GAFF

454.smi
OC1=CC=C(C=C1)C2=NN=C(O2)SCC#C

obabel -ismi 454.smi -O 454.mol2 --gen3D -h
obminimize -ff GAFF -o mol2 454.mol2 > 454-gaff.mol2

when -ff GAFF is omitted the results look ok.

Is this a bug or an omission in GAFF?
Anyway to detect of avoid these kind of issues with GAFF?


best wishes,

Eiso

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Re: distorted rings with obminimize -ff GAFF

David van der Spoel
On 09/01/17 16:08, Eiso AB wrote:

> (installation: Open Babel 2.4.0)
>
> I'm getting a distorted ring (the 5-ring) when using
> obminimize with -ff GAFF
>
> 454.smi
> OC1=CC=C(C=C1)C2=NN=C(O2)SCC#C
>
> obabel -ismi 454.smi -O 454.mol2 --gen3D -h
> obminimize -ff GAFF -o mol2 454.mol2 > 454-gaff.mol2
>
> when -ff GAFF is omitted the results look ok.
>
> Is this a bug or an omission in GAFF?
> Anyway to detect of avoid these kind of issues with GAFF?
Did you check whether the 3D structure looks OK? OK I verified it and it
is fine. An N-N bond in a ring is problematic for atom type detection
though. Indeed, detecting these problems should be trivial:

COULD NOT FIND PARAMETERS FOR BOND cp-nd, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR BOND cp-os, USING DEFAULT PARAMETERS
SETTING UP ANGLE CALCULATIONS...
COULD NOT FIND PARAMETERS FOR ANGLE ca-cp-nd, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR ANGLE ca-cp-os, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR ANGLE nd-cp-os, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR ANGLE cp-nd-nd, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR ANGLE nd-nd-cd, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR ANGLE nd-cd-os, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR ANGLE cp-os-cd, USING DEFAULT PARAMETERS
COULD NOT FIND PARAMETERS FOR ANGLE ss-c3-c1, USING DEFAULT PARAMETERS




>
>
> best wishes,
>
> Eiso
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
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> _______________________________________________
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> 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: distorted rings with obminimize -ff GAFF

Eiso AB-2
hmm, strange.
how do you look at the structure?
creating a svg with obabel and   -osvg actually seems to
repair the problem when the input is a mol2 file but not if it's a pdb file

could you try this:

obabel -ismi 454.smi -O 454.mol2 --gen3D -h
obminimize -ff GAFF -o pdb 454.mol2 > 454-gaff.pdb

and

rasmol 454-gaff.pdb

The attached screenshot is what I get.



On Mon, Jan 9, 2017 at 4:30 PM, David van der Spoel
<[hidden email]> wrote:

> On 09/01/17 16:08, Eiso AB wrote:
>> (installation: Open Babel 2.4.0)
>>
>> I'm getting a distorted ring (the 5-ring) when using
>> obminimize with -ff GAFF
>>
>> 454.smi
>> OC1=CC=C(C=C1)C2=NN=C(O2)SCC#C
>>
>> obabel -ismi 454.smi -O 454.mol2 --gen3D -h
>> obminimize -ff GAFF -o mol2 454.mol2 > 454-gaff.mol2
>>
>> when -ff GAFF is omitted the results look ok.
>>
>> Is this a bug or an omission in GAFF?
>> Anyway to detect of avoid these kind of issues with GAFF?
> Did you check whether the 3D structure looks OK? OK I verified it and it
> is fine. An N-N bond in a ring is problematic for atom type detection
> though. Indeed, detecting these problems should be trivial:
>
> COULD NOT FIND PARAMETERS FOR BOND cp-nd, USING DEFAULT PARAMETERS
> COULD NOT FIND PARAMETERS FOR BOND cp-os, USING DEFAULT PARAMETERS
> SETTING UP ANGLE CALCULATIONS...
> COULD NOT FIND PARAMETERS FOR ANGLE ca-cp-nd, USING DEFAULT PARAMETERS
> COULD NOT FIND PARAMETERS FOR ANGLE ca-cp-os, USING DEFAULT PARAMETERS
> COULD NOT FIND PARAMETERS FOR ANGLE nd-cp-os, USING DEFAULT PARAMETERS
> COULD NOT FIND PARAMETERS FOR ANGLE cp-nd-nd, USING DEFAULT PARAMETERS
> COULD NOT FIND PARAMETERS FOR ANGLE nd-nd-cd, USING DEFAULT PARAMETERS
> COULD NOT FIND PARAMETERS FOR ANGLE nd-cd-os, USING DEFAULT PARAMETERS
> COULD NOT FIND PARAMETERS FOR ANGLE cp-os-cd, USING DEFAULT PARAMETERS
> COULD NOT FIND PARAMETERS FOR ANGLE ss-c3-c1, USING DEFAULT PARAMETERS
>
>
>
>
>>
>>
>> best wishes,
>>
>> Eiso
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>> _______________________________________________
>> 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
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

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Re: distorted rings with obminimize -ff GAFF

David van der Spoel
On 09/01/17 17:57, Eiso AB wrote:
> hmm, strange.
> how do you look at the structure?
Generate an sdf with babel instead of a mol2 and then visualize with
avogadro (pdb with pymol works just as well).

We will look into the GAFF atom typing (my group did the last update).


> creating a svg with obabel and   -osvg actually seems to
> repair the problem when the input is a mol2 file but not if it's a pdb file
>
> could you try this:
>
> obabel -ismi 454.smi -O 454.mol2 --gen3D -h
> obminimize -ff GAFF -o pdb 454.mol2 > 454-gaff.pdb
>
> and
>
> rasmol 454-gaff.pdb
>
> The attached screenshot is what I get.
>
>
>
> On Mon, Jan 9, 2017 at 4:30 PM, David van der Spoel
> <[hidden email]> wrote:
>> On 09/01/17 16:08, Eiso AB wrote:
>>> (installation: Open Babel 2.4.0)
>>>
>>> I'm getting a distorted ring (the 5-ring) when using
>>> obminimize with -ff GAFF
>>>
>>> 454.smi
>>> OC1=CC=C(C=C1)C2=NN=C(O2)SCC#C
>>>
>>> obabel -ismi 454.smi -O 454.mol2 --gen3D -h
>>> obminimize -ff GAFF -o mol2 454.mol2 > 454-gaff.mol2
>>>
>>> when -ff GAFF is omitted the results look ok.
>>>
>>> Is this a bug or an omission in GAFF?
>>> Anyway to detect of avoid these kind of issues with GAFF?
>> Did you check whether the 3D structure looks OK? OK I verified it and it
>> is fine. An N-N bond in a ring is problematic for atom type detection
>> though. Indeed, detecting these problems should be trivial:
>>
>> COULD NOT FIND PARAMETERS FOR BOND cp-nd, USING DEFAULT PARAMETERS
>> COULD NOT FIND PARAMETERS FOR BOND cp-os, USING DEFAULT PARAMETERS
>> SETTING UP ANGLE CALCULATIONS...
>> COULD NOT FIND PARAMETERS FOR ANGLE ca-cp-nd, USING DEFAULT PARAMETERS
>> COULD NOT FIND PARAMETERS FOR ANGLE ca-cp-os, USING DEFAULT PARAMETERS
>> COULD NOT FIND PARAMETERS FOR ANGLE nd-cp-os, USING DEFAULT PARAMETERS
>> COULD NOT FIND PARAMETERS FOR ANGLE cp-nd-nd, USING DEFAULT PARAMETERS
>> COULD NOT FIND PARAMETERS FOR ANGLE nd-nd-cd, USING DEFAULT PARAMETERS
>> COULD NOT FIND PARAMETERS FOR ANGLE nd-cd-os, USING DEFAULT PARAMETERS
>> COULD NOT FIND PARAMETERS FOR ANGLE cp-os-cd, USING DEFAULT PARAMETERS
>> COULD NOT FIND PARAMETERS FOR ANGLE ss-c3-c1, USING DEFAULT PARAMETERS
>>
>>
>>
>>
>>>
>>>
>>> best wishes,
>>>
>>> Eiso
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>>> _______________________________________________
>>> 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
>>
>> ------------------------------------------------------------------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>> _______________________________________________
>> 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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Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
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