On Thu, Oct 21, 2021 at 7:22 AM Daniel Fowles <
daniel.fowles.2014.uni.strath.ac.uk> wrote:
> Hi,
>
> Ive recently updated from Ambertools18 to Ambertools21, and have found
> that the scripts I used to run tleap and antechamber no longer work even
> when run on the same systems. I have gone through the manual and cannot see
> what is going wrong.
>
> Ambertools18 and 21 scripts:
> General commands –
> antechamber -i 0001met.pdb -fi pdb -o gen.mol2 -fo mol2 -c bcc -s 2 -nc -1
> 2>&1 | tee antechamber.log
>
You are specifying the charge as -1 here.
> Ambertools18 output:
> Running: /opt/software/ambertools/intel_2017.1/18.0/bin/bondtype -j full
> -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> Running: /opt/software/ambertools/intel_2017.1/18.0/bin/atomtype -i
> ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> Info: Total number of electrons: 10; net charge: 0
>
The net charge here is 0, suggesting you didn't use the `-nc -1` flag with
AmberTools 18. 10 electrons and the `met.pdb` file name suggests to me
this is methane, which indeed should have a net 0 charge.
> Ambertools21 output:
> Running: /opt/software/ambertools/intel-2020.4/20.0/bin/bondtype -j full
> -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> Running: /opt/software/ambertools/intel-2020.4/20.0/bin/atomtype -i
> ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> Info: Total number of electrons: 11; net charge: -1
> Info: The number of electrons is odd (11).
> Please check the total charge (-nc flag) and spin multiplicity (-m
> flag).
>
Here the net charge is -1, giving the system an extra electron. While
there are obviously systems with spin multiplicity > 1, these are atypical
for organic molecules that antechamber is typically used on. If this
molecule really *is* methane, then the net charge should be set to 0, which
will fix this particular problem.
Pay careful attention to the output you get from the programs, as they
often contain information helpful to diagnosing the problem.
Good luck,
Jason
--
Jason M. Swails
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Received on Thu Oct 21 2021 - 06:00:03 PDT
