VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Fri Dec 03 2021 - 07:07:48 CST

Hi Bassam,

Can you be more specific about which build of VMD you are using? Support for lone pairs has only been in VMD for about a year, and will have an fftk version of 2.1. Assuming that you are using the latest version, please send me your files off-list so we can try to reproduce the error.

Best,
JC

On Dec 3, 2021, at 3:35 AM, Bassam Haddad <bhaddad_at_pdx.edu<mailto:bhaddad_at_pdx.edu>> wrote:

Hi all,

As stated in the subject line, VMD (1.4) is crashing due to a segmentation fault when I am "guessing" the charge groups, following the water-interaction calculation in ORCA. I generated diclofenac using CHARMM-GUI, and built a parameter file using FFtK. Due to the di-chloronated aromatic ring I have LP particles, which I believe should still work with FFtK.. though this isn't a problem I had when trying to parameterize other small molecules, so I thought perhaps this is the source of the problem. I am curious if anyone has an idea as to why this is happening, or if there is something I need to do differently when working with LP particles in halogenated species.

Thank you for your time, and help!

Best,
Bassam
________________________
Bassam Haddad, Ph.D.
Post-Doctoral Researcher
Forschungszentrum Juelich
Juelich, Germany