Re: Small molecule simulation error NAMD

From: José Villalaín (
Date: Wed Feb 24 2021 - 01:59:49 CST

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 ¡!.


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