[AMBER] AMBER G09 RESP Calculation problem

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Mon, 1 Jul 2019 11:22:54 +0000

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
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