Re: QMMM Question

From: Marcelo C. R. Melo (
Date: Tue Oct 18 2022 - 16:33:00 CDT

Hi Kelly,

NAMD offers the user the ability to run a second executable after each QM
calculation. This is used when there is a need to post-process the raw QM
output at each simulation step, instead of just using the gradients and
partial charges used in "regular" QM/MM simulations.

Your QwikMD setup must have accidentally set the "qmSecProc" keyword, so
all you need to do is remove it from your NAMD config files.


On Mon, Oct 17, 2022 at 3:42 PM Mcguire, Kelly <> wrote:

> I am running a test system using QwikMD to setup a quick QMMM with MOPAC.
> MOPAC is installed correctly and works fine. I run my QMMM using NAMD 2.14
> (non-CUDA) and it seems to run the QM part fine. I get a qmmm_0.input.out
> and there are no errors. But on the NAMD side, my log file gives the error:
> FATAL ERROR: Error running second command for QM calculation
> What second command is this referring to?
> Dr. Kelly McGuire
> Herzik Lab - Postdoc
> Chemistry/Biochemistry Department
> Natural Science Building, 4104A, 4106A, 4017

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