VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Fri Jan 12 2024 - 18:13:38 CST

Thanks for sending the files. The problem is that the naming scheme in your PDB does not match your PSF. There’s no resname in it, and the atom names don’t match. You need to create a PDB at the same time you make the PSF so that everything is in agreement.

With regards to the water clashes you mentioned, that is inevitably a problem for larger molecules. I don’t recall how we solved it in this case, but it might be described in the paper you mentioned. You can try optimizing without it, although a problem that arises then is that the optimizer will dump charge on that atom because it incurs relatively little penalty.

Best,
JC

> On Jan 9, 2024, at 10:54 PM, Gumbart, JC <gumbart_at_physics.gatech.edu> wrote:
>
> Hi Francesco,
>
> Can you please send me separately a set of files I can use to try to reproduce the error, including the ORCA output?
>
> Best,
> JC
>
>> On Jan 8, 2024, at 9:38 AM, francesco quilli <quilli.1855253_at_studenti.uniroma1.it> wrote:
>>
>> Hi all
>>
>> I am new to using FFTK and ORCA to parameterize a small molecule. After doing the ethanol tutorial, as a benchmark, I am attempting to replicate the results of the work of Pang et al (DOI: 10.1063/5.0022802).
>> I followed the guidelines of this work, recreating reduced structure for partial charges optimization and bond and angles optimization. I have been struggling to optimize the partial charges.
>> FFTK fails to run the optimization, and the following is the output:
>>
>> measure fit: selections must have the same number of atoms
>> measure fit: selections must have the same number of atoms
>> while executing
>> "measure fit $sel2 $sel1"
>> (procedure "::ForceFieldToolKit::ORCA::auxFit_ChargeOpt" line 6)
>> invoked from within
>> "::ForceFieldToolKit::${qmSoft}::auxFit_ChargeOpt $refmolid $resName"
>> (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 217)
>> 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..."
>>
>>
>> It appears that the input files have different number of atom. I have checked the psf, the pdb file obtained through geometry optimization,and all the QM calculation files, but apparently, they seems to have the same number of atoms.
>> Could anyone give me some advice or tips on this issue? I will be very grateful for any guidance.
>>
>> PS I'm using vmd 1.9.4 and ORCA 5.0.4
>>
>> Best,
>> Francesco
>
>