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From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Wed Nov 11 2020 - 23:48:15 CST
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Hi Nibedita,
Did the tutorial work for you? Can you try to narrow down what is different? If you can’t figure it out, you can send me files off list to try to reproduce it.
Best,
JC
On Nov 6, 2020, at 6:22 AM, Nibedita Ray Chaudhuri <nivirc.143_at_gmail.com<mailto:nivirc.143_at_gmail.com>> wrote:
Hello,
I am trying to parameterize a small molecule following the fftk tutorial using the fftk plugin of VMD version1.9.3, but I am getting the following error in the Opt. Charges step:
domain error: argument not in valid range
domain error: argument not in valid range
while executing
"expr { sqrt($epsA * $epsH) * ( pow(($rminA+$rminH)/$dH1,12) - 2.0*pow(($rminA+$rminH)/$dH1,6) ) + sqrt($epsA * $epsH) * ( pow(($rminA+$rminH)/$dH2..."
(procedure "::ForceFieldToolKit::ChargeOpt::computeIntE" line 46)
invoked from within
"::ForceFieldToolKit::ChargeOpt::computeIntE $i $j"
......................................
......................................
I have been following the earlier threads but I am not sure what is the specific problem in my case. I tried to do the same in the new version of VMD 1.9.4a48 but this time it shows:
ERROR) No molecules loaded.mol addfile operates on one molecule only
ERROR) No molecules loaded.mol addfile operates on one molecule only
while executing
"mol addfile $pdbPath waitfor all $cmpdMolID"
(procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 88)
invoked from within
"::ForceFieldToolKit::ChargeOpt::optimize"
(procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
invoked from within
"::ForceFieldToolKit::gui::coptRunOpt "
invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt invoke "
invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt instate {pressed !disabled} { .fftk_gui.hlf.nb.chargeopt.runOpt state !pressed; .fftk_gui.hlf.nb.chargeopt.runOpt in.."
(command bound to event)
I checked my PSF file and apparently, everything seems fine. Is there any way this problem can be resolved without having to edit the plugin code?
I am pretty lost here. So, any suggestions will be highly appreciated.
I am attaching the debugged log file. Please let me know if any more information is needed
Nibedita
<Charge-Opt.debug.log>
- Next message: Pang, Yui Tik: "Re: "atomsel: set: bad data in 0th element" ffTK"
- Previous message: B: "Re: Merge Structure changes coordinates to 0"
- In reply to: Nibedita Ray Chaudhuri: "Error in charge optimization"
- Next in thread: Gumbart, JC: "Re: Error in charge optimization"
- Reply: Gumbart, JC: "Re: Error in charge optimization"
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