VMD-L Mailing List

From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Fri Dec 03 2021 - 07:09:39 CST

Hi JC,

I realized I typed it incorrectly...

VMD 1.9.4a51 is the version that produced the error.

I just downloaded VMD 1.9.4a55 to replace it, and have restarted my
parameterization efforts.

Best,
Bassam

On Fri, Dec 3, 2021 at 2:07 PM Gumbart, JC <gumbart_at_physics.gatech.edu>
wrote:

> 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> 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
>
>
>