Re: [AMBER] amino-cyclopropyl parameters

From: Loris Moretti <>
Date: Tue, 30 May 2017 12:39:51 +0000

Thanks for the reply! I think I've found it.

In the gaff parameters file dat/leap/parm/gaff2.dat the line corresponding to the angle term I need is:

cx-cx-n3 114.892 59.590 SOURCE4_SOURCE5 400 0.3281

where according to the first column are the atom types of the angle, the second is the harmonic force constant and the third is equilibrium bond angle in degrees.

In the literature one can find that such angle should be around 114 degrees. So, my guess is that the 2 values have been exchange by mistake, in fact once replaced the simulation went fine.

I'm not an expert and I hope that someone more experienced than me would take a look.



From: Thakur, Abhishek <>
Sent: Friday, May 26, 2017 3:00:04 PM
To: AMBER Mailing List
Subject: Re: [AMBER] amino-cyclopropyl parameters

Hi Loris
For this I will suggest you to optimize your ligand using gaussian first and then calculate RESP charge. Then using those file try to generate your parameters for ligand

With regards,

Sent using OWA for iPhone
From: Loris Moretti <>
Sent: Thursday, May 25, 2017 8:32:30 PM
Subject: [AMBER] amino-cyclopropyl parameters

Hi All,

I have a ligand containing a cyclopropyl substituted with an amine group and I would like to simulate its dynamic behavior inside a protein.

But the parameters I get from the usual procedure antechamber + parmck result in a distorted molecule. Here in attachment the minimal example as an initial molecule (ligand.mol2) with AM1-BCC charges, the ligand.frcmod produced by the command:

parmchk2 -i ligand.mol2 -f mol2 -o ligand.frcmod -s 2

(from Ambertools17)

I've also tried with parmchk (instead of parmchk2) and gaff (instead of gaff2) without improvement. The "leap" commands to produce the system and the parameters and the coordinates for the system (system_init.prm and system_init.crd). The for the simulation settings and the trajectory system_md.cdf obtained with the command:

sander -O -i -o md.out -p system_init.prm -c system_init.crd -r system_md.rst -x system_md.cdf

In the simulation is clear that the angle of the C-C-N (carbons of the cycle and the nitrogen) goes distorted and I understand I have to insert new parameters for such angle into the ligand.frcmod file. I guess I have to generate those values manually, how should I do that? I've tried to check but I couldn't find proper information about the procedure.

Thanks in advance,


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Received on Tue May 30 2017 - 06:00:02 PDT
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