Re: Small molecule simulation error NAMD

From: Chathuranga Siriwardhana (
Date: Wed Feb 24 2021 - 11:34:37 CST

Hi all,
Thank you so much for your responses for my issue. I was able to run the
simulation with lone pairs.
However when the psf file is generated using psfgen 2.0 it contains a bond
between the lone pair and the halogen. CgenFF does not contain bond
parameters for Halogen Lone pair. (May be I was doing something wrong since
I'm really new to this field)
I set up the simulation by generating psf files using both psfgen 1.6.4
(this version does not generate the bond between lone pair and the halogen
or the NUMLP section ) and psfgen 2.0 which generates the NUMLP section.
Then produced a combined psf file manually without halogen - lone pair bond
but with the NUMLP section.

Thanks again and I appreciate all of yours help through this mailing list


On Wed, Feb 24, 2021 at 3:09 AM José Villalaín <> wrote:

> Dear all,
> First of all, sorry for any duplicate mail I might have sent, we have had
> some problems with our university mail in the past few days .... I have
> unsubscribed and subscribe again. I hope that now it is possible for me to
> send mails to the list.
> The last mail I tried to sent to the list read the following,
> *I have recently run into the same problem, i.e., using NAMD 2.14 and a
> small molecule containing a chlorine atom. In my opinion to obtain the pdb
> / psf pair it is best to use Charmm-Gui / Ligand Reader with the molecule
> previously built by using Marvin Sketch (to obtain the mol2/pdb/sdf files).
> I have been able to minimize my system, but it has been impossible for me
> to equilibrate it. The error I obtained was the always same, i.e., atom
> moving to fast (referring to the lone pair). It has been impossible for me
> to go on besides trying everything in hand ....*
> Additionally, I would like to say that the psf file I obtained through
> Charmm-Gui contained the " !NUMLP NUMLPH" instruction joining the chloride
> atom with the lone pair.
> Last by no least, thanks a lot to everyone for you continuous help and the
> owner of the list for your work on developing NAMD ¡!.
> José

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