VMD-L Mailing List

From: Pang, Yui Tik (andrewpang_at_gatech.edu)
Date: Tue Dec 07 2021 - 15:12:20 CST

Hi Bassam,

Sorry for the inconvenience but ffTK expects the lone pairs to be explicitly bonded to their parent atoms in the current implementation. You can either add it by hand, or use the BuildPar tab of ffTK to build a psf with the expected format from the CGenFF output.

Best,
Andrew
________________________________
From: Bassam Haddad <bhaddad_at_pdx.edu>
Sent: Tuesday, December 7, 2021 4:18 AM
To: Pang, Yui Tik <andrewpang_at_gatech.edu>
Subject: Re: vmd-l: FFTK segmentation fault when guessing charge groups

Hi Andrew,

Thanks for your response, I have attached a folder with the relevant files. Unfortunately, an error isn't reported; it just crashes when I try to 'guess' the charge groups.
My assumption is that it's due to the fact that I have LP particles, as I was able to get past this point when attempting to parameterize salicylate. I got the same problem when using VMD 1.9.4a51 and VMD 1.9.4a55.

Best,
Bassam

p.s. I sent these same files to JC, not sure if you are in the same lab or not. Thank you for your help!

On Fri, Dec 3, 2021 at 4:05 PM Pang, Yui Tik <andrewpang_at_gatech.edu<mailto:andrewpang_at_gatech.edu>> wrote:

Hi Bassam,

Do you mind sharing your files with me off-list so I can better assess the source of the error?

Thanks!

Andrew (Yui Tik Pang)

From: owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu> <owner-vmd-l_at_ks.uiuc.edu<mailto:owner-vmd-l_at_ks.uiuc.edu>> on behalf of Bassam Haddad <bhaddad_at_pdx.edu<mailto:bhaddad_at_pdx.edu>>
Sent: Friday, December 3, 2021 3:35:30 AM
To: VMD Mailing List <vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>
Subject: vmd-l: FFTK segmentation fault when guessing charge groups

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


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