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
<sp...@xray.bmc.uu.se> 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
>>
>> ------------------------------------------------------------------------------
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>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> sp...@xray.bmc.uu.se http://folding.bmc.uu.se
>
> ------------------------------------------------------------------------------
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