Hi,
I'm not sure if there are any remaining/unresolved issues,
so let me review:
1.
> /Users/guolaa/SOFTWARE/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
As Dave wrote, this is expected output for a fatal error situation.
This is the start of the fatal error message. It gives the full path
of the executable that is emitting the error message. That can be very
useful in scripting contexts, so i am reluctant to tweak it. I am happy
to document it here (and by adding an example to the manual and updating
tutorials). To repeat, antechamber lives in bin/to_be_dispatched.
2.
> Number of arguments is odd - arguments must come in pairs.
This part of the error message is perhaps more cryptic. I'll try to
tweak it. (Here's what i think happened: ac_input and input are undefined
and I'm guessing so was INP; so this:
guolaa$ antechamber -i $ac_input/$input.pdb -fi pdb -o $input.prepi -fo prepi -c bcc -rn $INP
becomes this:
guolaa$ antechamber -i /.pdb -fi pdb -o .prepi -fo prepi -c bcc -rn
and thus -rn does not have an argument, so the total argument count is odd.)
3.
> This time is was an incorrect molecular abbreviation that seemed to cause the error:
...
> Cannot properly run "/Users/guolaa/SOFTWARE/amber18/bin/sqm -O -i sqm.in -o sqm.out".
I think you are indicating that you know why sqm failed.
If that is not the case then this is the only remaining issue.
If you need help on this then send more detail, esp. the original pdb file
and sqm.out. It's probably worth starting a whole new thread unless you have
comments on 1 and 2 above.
scott
On Wed, May 02, 2018 at 12:53:36PM +0000, Gustaf Olsson wrote:
> Right. So, since I can???t go on working I just had to see if I could recreate the issue and I did.
>
> I am assuming the answer to this one will be the same as for antechamber. Since I did not document the issue properly last time and just ???guessed??? what the output was, I apparently missed the "Fatal Error!??? declaration, being this now I would assume that this is just as much of an non issue as the antechamber error.
>
> This time is was an incorrect molecular abbreviation that seemed to cause the error:
>
> Welcome to antechamber 17.3: molecular input file processor.
>
> acdoctor mode is on: check and diagnosis problems in the input file.
> -- Check Format for pdb File --
> Status: pass
> -- 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.
>
> Info: Total number of electrons: 0; net charge: 0
>
> Running: /Users/guolaa/SOFTWARE/amber18/bin/sqm -O -i sqm.in -o sqm.out
> /Users/guolaa/SOFTWARE/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
> Cannot properly run "/Users/guolaa/SOFTWARE/amber18/bin/sqm -O -i sqm.in -o sqm.out".
>
> It???s just the fatal error that is called from "to_be_dispatched/antechamber??? right?
>
> Anyway, thank you for you help and input, let me know if there is anything I can do to help further.
> // Gustaf
>
> On 2 May 2018, at 13:48, David A Case <david.case.rutgers.edu<mailto:david.case.rutgers.edu>> wrote:
>
> On Wed, May 02, 2018, Gustaf Olsson wrote:
>
> /Users/guolaa/SOFTWARE/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
> Number of arguments is odd - arguments must come in pairs.
>
> Antechamber does point to the correct location however the error for
> antechamber refers to ???to_be_dispatched???.
>
> This is expected behavior: the actual antechamber binary executable
> lives in $AMBERHOME/bin/to_be_dispatched. I think the reference to
> "to_be_dispatched" is unlikely to cause much confusion, but it may be
> that we can tweak the "Fatal error" message.
>
> Note that the binary file for sqm does *not* reside in to_be_dispatched,
> and the error you reported for it was different than the one above. I
> guess we still don't know how the sqm problem arose.
On Wed, May 02, 2018 at 06:44:30AM +0000, Gustaf Olsson wrote:
> This is the direct output by running antechamber without correct input, I intentionally ignored to set ???ac_input??? and ???input??? which I used before to run multiple structures in sequence. As you can se, $AMBERHOME and $AMBER_PREFIX is set
>
> guolaa$ echo $AMBERHOME $AMBER_PREFIX
> /Users/guolaa/SOFTWARE/amber18 /Users/guolaa/SOFTWARE/amber18
> guolaa$ antechamber -i $ac_input/$input.pdb -fi pdb -o $input.prepi -fo prepi -c bcc -rn $INP
>
> Welcome to antechamber 17.3: molecular input file processor.
>
> /Users/guolaa/SOFTWARE/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
> Number of arguments is odd - arguments must come in pairs.
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Received on Wed May 02 2018 - 18:00:03 PDT
