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From: BLUNTZER Marie
Sent: 08 October 2020 11:50
To: AMBER Mailing List <amber.ambermd.org>
Subject: partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule
good morning
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.
Then I am using antechamber to compute the RESP
using the command
antechamber -i %s.log -fi gout -o %s.mol2 -fo mol2 -c resp -at amber -eq 2 -pf -dr n at
which as I understand it, calls a certain number of background scripts and notably the resp command
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 when building the ANTECHAMBER_RESP1.IN and ANTECHAMBER_RESP2.IN files and equivalent atoms did not return identical charges.
I tweaked and decomposed the antechamber command replacing the resp input by the ones of a conformers that had picked up the symmetry and that gave me the expected output, but that is a bit troublesome ...
Is that a bug? Has it been fixed in more recent versions of antechamber ?
I have attached the conformer 1 (conformer where antechamber picked up the symmetry) and the conformer 13 where the symmetry was not picked up
Best
Marie
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
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Received on Mon Oct 12 2020 - 04:30:02 PDT
