VMD-L Mailing List

From: Sarthak Mohanty (sarthakmohanty997_at_gmail.com)
Date: Mon Feb 26 2024 - 02:19:07 CST

Hello everyone :)

I am trying to learn ffTK because I have to perform an MD simulation on a
protein-ligand system and I am unable to get good parameters for my ligand
from online CGenFF servers. I am following the ffTK tutorial (updated for
ORCA) which I found on Mariano Spivak's page (
http://www.ks.uiuc.edu/~mariano/fftk-tutorial.pdf).

I followed the tutorial and designed my ligand molecule in Molefacture 2.0.
I am using VMD 1.9.4a57 on Ubuntu (64 bit) since VMD 1.9.3 does not have
Molefacture 2.0. However, when I try to write the structure of my ligand
into PSF and PDB file, I get the following error message:

couldn't open "/home/freax/qwikmd/toppar/toppartable.txt": no such file or
directory
couldn't open "/home/freax/qwikmd/toppar/toppartable.txt": no such file or
directory
    while executing
"open ${folder}/toppar/toppartable.txt w+"
    (procedure "QWIKMD::checkDeposit" line 97)
    invoked from within
"QWIKMD::checkDeposit 0"
    (procedure "Molefacture::loadDefaulTopo" line 17)
    invoked from within
"Molefacture::loadDefaulTopo $resnames"
    (procedure "::Molefacture::write_psfpdbfiles" line 27)
    invoked from within
"::Molefacture::write_psfpdbfiles"
    invoked from within
".molefac.topframe.menubar.file.menu invoke active"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke active]"
    (procedure "tk::MenuInvoke" line 50)
    invoked from within
"tk::MenuInvoke .molefac.topframe.menubar.file.menu 1"
    (command bound to event)

I followed the tutorial instructions exactly with no mistakes, so I don't
know why I am getting this error. Can someone please help me understand why
I am getting this error and how to fix it?
I will be very grateful if someone can help me with this.

Thank you so much.

-Sarthak