So, it turns out that the g09 program I have access to has not been updated since, well 2009. So it is still on rev. A.02 which explains why I am not seeing the intended output. Hence, I have to revert to using the g03 syntax.
I wish all of you a fantastic rest of your day and my apologise for the interruption
// Gustaf
> On 1 Jul 2019, at 13:22, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> So I started trying to use g09 to perform some charge calculations today and I ran into some issues.
>
>
> Looking at the manual I managed to put together the following general input:
>
> $ antechamber -i input.pdb -fi pdb -o input.gcrt -fo gcrt -gn "%nproc=8” -ch input.chk -gv 1 -ge input.gesp
>
> Producing files similar to the following the following
>
> --Link1--
> %nproc=8
> %chk=input.chk
> #HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt
> # iop(6/50=1)
>
> remark line goes here
>
> 0 1
> C 2.7610000000 -2.7670000000 -1.8530000000
> C 1.8600000000 -2.1670000000 -1.0600000000
> …
> ...
> H 1.3620000000 -0.7540000000 1.9070000000
>
> input.gesp
>
> input.gesp
>
> I did some reading and realised that something is not really looking right as iop(6/33=2) has been completely replaced by iop(6/50=1) in g09 after whatever version and iop(6/42=6) is structure dependent. However, before starting to change to much I decided to just run the default first and see what happens.
>
> $ g09 input.gcrt
>
> This produces two new files:
>
> input.chk
> input.log
>
> As you can see, there is no “gesp” file produced. Now, am I missing something or doing something wrong? Because all I see is the “log” file which is not a “gesp” file as antechamber breaks on execution of the following:
>
> $ antechamber -i input.log -fi gesp -o input.prepi -fo prepi -c resp -eq 2
>
> Welcome to antechamber 19.0: molecular input file processor.
>
> acdoctor mode is on: check and diagnose problems in the input file.
> -- Check Unusual Elements --
> Status: pass
> -- Check Open Valences --
> Warning: This molecule has no hydrogens nor halogens.
> It is quite possible that there are unfilled valences.
> -- Check Geometry --
> for those bonded
> for those not bonded
> Status: pass
> -- Check Weird Bonds --
> Status: pass
> -- Check Number of Units --
> Status: pass
> acdoctor mode has completed checking the input file.
>
>
>
>
> /amber18/bin/to_be_dispatched/antechamber: Fatal Error!
> Unable to find charges in file (QOUT).
> Verify the filename and the file contents.
>
> I figured out that I can produce the intended prep file using the “old” format of the command:
>
> $ antechamber -i input.log -fi gout -o input.prepi -fo prepi -c resp -eq 2
>
> Though I cannot figure out what I am doing wrong as I am not getting the "gesp” file as intended.
>
>
> Any suggestions regarding getting the correct/intended files produces to be able to reproduce and run the suggested commands as in the manual?
>
> Best regards
> // Gustaf
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Received on Mon Jul 01 2019 - 05:30:02 PDT
