Re: [AMBER] LEaP Not Reading a Parameter in .frcmod File

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Thu, 24 Feb 2022 10:00:02 -0500

the problem is that you've listed a negative periodicity for o-c-N-H, which
tells it to read the next line into the same dihedral. However, your next
line is the o-c-N-CX. So you need to either add more terms to o-c-N-H, or
make the PN positive.
as an aside, why do you use a divider of 4 for o-c-N-CX? It's unlikely that
there are 4 sets of this term around that c-N bond.

DIHE
o-c-N-H 1 2.500 180.0 -2.000
o-c-N-CX 4 10.000 180.0 2.000


take a look at this for format details:
https://ambermd.org/FileFormats.php#parm.dat 
--
Carlos Simmerling, Ph.D. (he, him, his)
Marsha Laufer Endowed Professor of Physical and Quantitative Biology
Professor, Department of Chemistry
Associate Director, Laufer Center for Physical and Quantitative Biology
Room 119 Laufer Center, Stony Brook University, Stony Brook, NY 11794-5115
http://www.simmerlinglab.org
On Thu, Feb 24, 2022 at 9:50 AM Nathan Black <nathanblack262.gmail.com>
wrote:
> Hello AMBER Users,
>
> I recently posted here regarding the mixing of force fields  (in my
> specific case, GAFF2 and ff14SB) on a single residue. Thanks to the
> assistance of of Dr. Anselm Horn and Mr. Carlos Simmerling, I was able to
> develop a workflow that accomplishes this. However, I have run into a
> separate issue during its implementation that I believe warrants its own
> thread.
>
> I have written a .frcmod file that contains manually-input parameters at
> the surfactant head-tail boundary. However, when trying to save parameter
> topology and coordinate files for these surfactants in LEaP, I am given the
> error:
>
> Error: **no torsion terms for o-c-N-CX.
>
> However, this parameter is accounted for in the .frcmod file I created. I
> suspect I have formatted the file incorrectly, but then my other manual
> torsion parameters are read without issue.
>
> I have attached a cleaned (single-attempt) leap.log file, as well as the
> .frcmod file I wrote. Any assistance is much appreciated!
>
> -NDB
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Received on Thu Feb 24 2022 - 07:30:02 PST
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