Using the coordinates you posted, it would appear that molecules 1 and 13
are both of point group C1 (determined using Chemcraft). Were you expecting
something different?
Why are you using symmetry with G9? The possible reduction in compute time
is minimal, especially when the molecules are both point group C1.
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-----Original Message-----
From: BLUNTZER Marie <s1772078.sms.ed.ac.uk>
Sent: Monday, October 12, 2020 8:43 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] partial charge calculation (RESP) using
gaussian09/antechamber (ambertools17) on a symmetrical molecule
Can you see the attached files ? gaussian output files are too big, if
attached, the message bounce back.
conformer 13 is one conformer where the symmetry was not picked up
* 13.gau is the input from gaussian,
* asym_ANTECHAMBER_RESP1.IN and asym_ANTECHAMBER_RESP2.IN are the
intermediate files generated by antechamber for this system
* 13.mol2 is the output from antechamber with partial charges.
conformer 1 is one conformer where the symmetry was picked up and
respectively I attached 1.gau, sym_ANTECHAMBER_RESP1.IN,
sym_ANTECHAMBER_RESP2.IN, and 1.mol2.
Best
Marie
________________________________
From: BLUNTZER Marie <s1772078.sms.ed.ac.uk>
Sent: 12 October 2020 13:34
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] partial charge calculation (RESP) using
gaussian09/antechamber (ambertools17) on a symmetrical molecule
Can you see the attached files ? gaussian log files are quite big so I the
message bounced back few times
conformer 13 is one conformer where the symmetry was not picked up
* 13.log is the output from gaussian,
* asym_ANTECHAMBER_RESP1.IN and asym_ANTECHAMBER_RESP2.IN are the
intermediate files generated by antechamber for this system
* 13.mol2 is the output from antechamber with partial charges.
conformer 1 is one conformer where the symmetry was picked up and
respectively I attached 1.log, sym_ANTECHAMBER_RESP1.IN,
sym_ANTECHAMBER_RESP2.IN, and 1.mol2.
this thread is just to report the issue, I have found a way around the
problem.
Best
Marie
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: 12 October 2020 13:06
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] partial charge calculation (RESP) using
gaussian09/antechamber (ambertools17) on a symmetrical molecule
On Mon, Oct 12, 2020, BLUNTZER Marie wrote:
>
>I am computing the MEP/ESP using gaussian09 of 100 conformers
>(generated using RDkit) of a symmetrical molecule using the HF/6-31* basis
set.
>
>On my system it picked up the symmetry for 81 conformers returning me
>identical partial charges for equivalent atoms but for 19 conformers
>the symmetry was not picked up
>
>I have attached the conformer 1 (conformer where antechamber picked up
>the symmetry) and the conformer 13 where the symmetry was not picked up
I have not seen this problem reported before. It would be helpful to see
the two conformers involved.
...thanks...dac
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Received on Mon Oct 12 2020 - 16:00:01 PDT
