The function your input is calling is actually RegExpFileSearch() right
above where I pointed you, but again it makes use of ent = readdir().
There's a comment in there about "returns an alphabetized list" but I may
not have gotten to that last bit, which would be what caused your alarm.
Dave
On Tue, Jun 13, 2017 at 12:23 AM, David Cerutti <dscerutti.gmail.com> wrote:
> Sorry I didn't see this earlier! Here's what happening. The energies are
> not being extracted in random order, but rather an order which matches the
> resulting trajectory. In this sense, the energies will be properly
> attributed to each conformation so long as you read the energies_mdgx.dat
> file along with the trajectory. Try converting the coordinates Coords.cdf
> to PDB / ascii and verifying that the frames match:
>
> cat > conv.ptrj << EOF
> trajin Coords.cdf
> trajout Coords.pdb pdb
> go
> EOF
>
> There should be no problem, I've checked over this specifically. Back
> when I did this same chore with a python script, the ordering got mangled
> by the imported glob library. When I actually sat down to write it in
> proper C code, I began to see the issues. At bottom, the computer doesn't
> alphabetize or numeratize things the way you do. If you wish to see under
> the hood, look in AmberTools/src/mdgx/Parse.c for DirectoryFileSearch(),
> and find the following:
>
> while ((ent = readdir(dir)) != NULL) {
> ...
> }
>
> It's that ent = readdir() operation that I'm reliant upon, which glob is
> probably reliant upon, and which you might use yourself if you need to
> write a directory scanning function at some time in the future. It will
> list each file in the directory, but not in the order you might expect. I
> simply make sure to extract coordinates and energies from one file at a
> time and keep them in the order they were read, while culling the bad data
> points.
>
> Try running a simple parameterization with energies_mdgx.dat and
> Coords.cdf, and you should be able to get sane results (errors <= 3-4
> kcal/mol once you include all the parameters relevant to the configurations
> you've generated). Let me know if you don't!
>
> Dave
>
>
> On Mon, Jun 12, 2017 at 9:36 AM, Charles-Alexandre Mattelaer <
> camattelaer01.gmail.com> wrote:
>
>> Dear Amber users
>>
>> As I already mentioned, I'm using mdgx to generate parameters for modified
>> nucleic acids. However, after extraction of the energies calculated by
>> ORCA, the resulting 'energies_mdgx.dat' file listed the calculated
>> energies
>> in random(?) order.I'm not quite sure what is happening here since the
>> extraction should be fairly simple (enclosed file '04_ExtractEnergies').
>> Using a 'for'-loop with the command sed I generated my own
>> 'energies_sed.dat' file for comparison.
>>
>> I enclosed the first of the ORCA outputs (Conf1.oout) so you can verify
>> that this energy does not show up as the first entry in the
>> 'energies_mdgx.dat' file. I also enclosed my own extracted
>> 'energies_sed.dat' file where this is correctly performed.
>>
>> Additionally, I can add that during the generation of the conformers (also
>> using mdgx) I lose several conformations so that I don't have 'Conf1.orca'
>> to 'ConfN.orca' consecutively, resulting in several empty 'ConfX.oout'
>> files since ORCA is called consecutively in a 'for'-loop. I don't know if
>> this should bother mdgx during extraction to throw the energies around?
>>
>> I assume this influences the parameter fitting stage, since the energies
>> should be attributed respectively to the conformation in the trajectory
>> file?
>>
>> Kind regards
>>
>> Charles-Alexandre Mattelaer
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
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Received on Mon Jun 12 2017 - 22:00:02 PDT
