VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Apr 16 2021 - 04:36:38 CDT

Hi all
I am faced by the following error while executing autopsf with a
nucleotide-protein system at the Guess/Spl;it Chains level (a 30A sphere
cut around the small-molecule ligand)
VMD 1.9.4a51
vecsub: two vectors don't have the same size
vecsub: two vectors don't have the same size
    while executing
"vecsub $x $y"
    (procedure "vecdist" line 2)
    invoked from within
"vecdist $Ccoords $Ncoords"
    (procedure "split_protein_and_water_pdb" line 250)
    invoked from within
"split_protein_and_water_pdb "${basename}-temp.pdb""
    (procedure "::autopsf::aftersels_gui" line 55)
    invoked from within
"::autopsf::aftersels_gui"
    invoked from within
".autopsf.sels.next invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 22)
    invoked from within
"tk::ButtonUp .autopsf.sels.next"
    (command bound to event)

I added the parameters for the ligand (which, for the ligand alone worked
well, also for MD), and
top_all36_cgenff.rtf
top_all36_lipid.rtf
top_all36_na.rtf
top_all36_prot.rtf
toppar_water_ions.str

Then, with "Everything" selected I clicked on Guess and split chains,
getting the above error.

I found no errors in the pdb file with VMD Jmol CHIMERA. Histidine was
assigned charmm names. Ligand pdb was in accordance with its psf/pdb. The
only other hetero was MG.

Thanks for any suggestion on what else I could check.

francesco pietra
I had a similar error in the past for another nucleotide-protein ensemble,
but only for a sphere of 60A, while 30A - which went on without errors -
was enough. I did not pursue that error further.