VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Wed Dec 30 2020 - 18:25:03 CST

I’m not sure about the lack of an outFile, but it seems this is the real issue: "The number of charges read from the resp run do not match the number in the currently loaded PSF file”

I noticed the molecule in the files you sent was quite large. I assume that isn’t the one you used for parameterization, so please check again when loading everything that they match up.

Best,
JC

On Dec 30, 2020, at 6:52 PM, Emma Wu <ewu20_at_illinois.edu<mailto:ewu20_at_illinois.edu>> wrote:

Hi JC,
I did what you recommended and left only the input name in the "Input Files Basename" and it solved the Fortran runtime error. However, I am getting this error instead:

an't read "outFile": no such variable
can't read "outFile": no such variable
    while executing
"puts $outFile "\nffTK has halted on error. The number of charges read from the resp run do not match the number in the currently loaded PSF file.\n""
    (procedure "::ForceFieldToolKit::ChargeOpt::ESP::updatePSF" line 28)
    invoked from within
"::ForceFieldToolKit::ChargeOpt::ESP::updatePSF"
    invoked from within
".fftk_gui.hlf.nb.optESP.runESP.runESP invoke "
    invoked from within
".fftk_gui.hlf.nb.optESP.runESP.runESP instate !disabled { .fftk_gui.hlf.nb.optESP.runESP.runESP invoke } "
    invoked from within
".fftk_gui.hlf.nb.optESP.runESP.runESP instate pressed { .fftk_gui.hlf.nb.optESP.runESP.runESP state !pressed; .fftk_gui.hlf.nb.optESP.runESP.runESP in..."
    (command bound to event)

Thank you so much in advance for your help!

Best,
Emma

On Mon, Dec 28, 2020 at 8:39 PM Gumbart, JC <gumbart_at_physics.gatech.edu<mailto:gumbart_at_physics.gatech.edu>> wrote:
Thanks Emma for sending your files. It worked for me using resp in Linux, although I also noticed that the file name gets cut at 80 characters in the output (right at “De”). So it’s clearly related to the path length.

It looks like that inputName gets set from the field “Input Files Basename” under the Opt. ESP tab. So if you remove the full path here and just leave the resname, it might work. If not, just try manually editing all of the input files to remove the full path, leaving only the file name at each instance it appears. Then click “Calc. RESP Charges”.

Best,
JC

> On Dec 28, 2020, at 1:20 AM, Gumbart, JC <gumbart_at_physics.gatech.edu<mailto:gumbart_at_physics.gatech.edu>> wrote:
>
> Hi Emma,
>
> I wonder if the path is too long? Or perhaps the error just cut it off:
>> At line 336 of file /Users/runner/miniforge3/conda-bld/ambertools_1603107085423/work/AmberTools/src/etc/resp.F (unit = 5, file = '/Volumes/Backup Plus/FileHistory/emmachenwu/PTH-40518/Data/C/Users/emmachenwu/De')
>
>
> Can you send me separately the files FFTK generated for input to RESP so that I can try them?
>
> Best,
> JC
>
>> On Dec 27, 2020, at 11:00 PM, Emma Wu <ewu20_at_illinois.edu<mailto:ewu20_at_illinois.edu>> wrote:
>>
>> Hi,
>> I am trying to use RESP in ffTK in the charge optimization step. I've gotten RESP from AmberTools. Here is the error I am getting with RESP:
>>
>> At line 336 of file /Users/runner/miniforge3/conda-bld/ambertools_1603107085423/work/AmberTools/src/etc/resp.F (unit = 5, file = '/Volumes/Backup Plus/FileHistory/emmachenwu/PTH-40518/Data/C/Users/emmachenwu/De')
>> Fortran runtime error: End of file
>>
>> Error termination. Backtrace:
>> #0 0x17d7089cc
>> #1 0x17d709a05
>> #2 0x17d70a24e
>> #3 0x17d9a1cfd
>> #4 0x17d9a262c
>> #5 0x17d99c2e2
>> #6 0x17d9a3d27
>> #7 0x17d9a4e74
>> #8 0x101c47774
>> #9 0x101c495ed
>> #10 0x101c4978a
>> At line 336 of file /Users/runner/miniforge3/conda-bld/ambertools_1603107085423/work/AmberTools/src/etc/resp.F (unit = 5, file = '/Volumes/Backup Plus/FileHistory/emmachenwu/PTH-40518/Data/C/Users/emmachenwu/De')
>> Fortran runtime error: End of file
>>
>> Error termination. Backtrace:
>> #0 0x17d7089cc
>> #1 0x17d709a05
>> #2 0x17d70a24e
>> #3 0x17d9a1cfd
>> #4 0x17d9a262c
>> #5 0x17d99c2e2
>> #6 0x17d9a3d27
>> #7 0x17d9a4e74
>> #8 0x101c47774
>> #9 0x101c495ed
>> #10 0x101c4978a
>> while executing
>> "::exec /Users/emmawu/anaconda3/bin/resp -O -i {/Volumes/Backup Plus/FileHistory/emmachenwu/PTH-40518/Data/C/Users/emmachenwu/Desktop/AutoDock/paramter..."
>> ("eval" body line 1)
>> invoked from within
>> "eval ::exec [list $exec_path] [lrange $args 1 end]"
>> (procedure "::ExecTool::exec" line 14)
>> invoked from within
>> "::ExecTool::exec $respPath -O -i ${inputName}.in -o ${inputName}.out -p ${inputName}.pch -t ${inputName}.chg -q ${inputName}.qin -e ${inputName}.dat"
>> (procedure "::ForceFieldToolKit::ChargeOpt::ESP::runESP" line 46)
>> invoked from within
>> "::ForceFieldToolKit::ChargeOpt::ESP::runESP"
>> invoked from within
>> ".fftk_gui.hlf.nb.optESP.runESP.runESP invoke "
>> invoked from within
>> ".fftk_gui.hlf.nb.optESP.runESP.runESP instate !disabled { .fftk_gui.hlf.nb.optESP.runESP.runESP invoke } "
>> invoked from within
>> ".fftk_gui.hlf.nb.optESP.runESP.runESP instate pressed { .fftk_gui.hlf.nb.optESP.runESP.runESP state !pressed; .fftk_gui.hlf.nb.optESP.runESP.runESP in..."
>> (command bound to event)
>>
>> I am not sure what this error is? Any and all help is appreciated! Thanks!
>>
>> Best,
>> Emma
>
>