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 - 04:30:03 PDT
