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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- chemical/x-mol2 attachment: 1.mol2
- chemical/x-mol2 attachment: 13.mol2
- chemical/x-gaussian-input attachment: 13.gau
- chemical/x-gaussian-input attachment: 1.gau
Received on Mon Oct 12 2020 - 06:00:04 PDT
