Dear David,
Thank you for looking into my problem and replying to my query.
> Indeed, if you look at the bonds to atom 7:
>
> 10 6 7 ar
> 11 7 8 ar
> 12 7 10 2
>
I understand about your concern and I agree that this looks unusual and
supposed to be carbon (7) not having valency of 5. and thats why after
converting this mol2 into ac file, I manually edited bond orders. I
suggest you to look into 'isg_singleDouble.ac'
Also, I request you to make prepi file using PDB you generated and above
ac file. I am really curious to know whether it works fine or not, as I
am using combination of amber16 and AmberTools16. Probably outcome might
be interesting for you as well.
PS: I tried exporting mol2 from various known editors like maestro-11,
chemdraw-16 and avogadro-1.2 (openbabel-2.3.2.)
Many thanks,
Ashish
On Thu, 2017-06-15 at 15:29 -0400, David Case wrote:
> On Thu, Jun 15, 2017, Ashish Radadiya wrote:
> >
> > I tested mol2 file with "acdoctor" it also gave bunch of warnings.
>
> Here's what I get with AmberTools17:
>
> slater% antechamber -i isg.mol2 -fi mol2 -o dac.mol2 -fo mol2
>
> Welcome to antechamber: molecular input file processor.
>
> acdoctor mode is on: check and diagnosis problems in the input file.
> -- Check Format for mol2 File --
> Status: pass
> -- Check Unusual Elements --
> Status: pass
> -- Check Open Valences --
> Status: pass
> -- Check Geometry --
> for those bonded
> for those not bonded
> Status: pass
> -- Check Weird Bonds --
> /home/case/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
> Weird atomic valence (5) for atom (ID: 7, Name: C4).
> Possible open valence.
>
> Indeed, if you look at the bonds to atom 7:
>
> 10 6 7 ar
> 11 7 8 ar
> 12 7 10 2
>
> You are asking for two aromatic bonds and one double bond to atom 7. This
> adds up to 5 (1.5 + 1.5 + 2), just like the error message says.
>
> I don't know how you got the mol2 file; for converting this to a pdb file
> (which has no bond-order information), then using that as input to antechamber
> worked fine for me.
>
> ....hope this helps....dac
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 16 2017 - 03:00:02 PDT
