Re: [AMBER] DNA force field.

From: Matias Machado <>
Date: Sat, 10 Aug 2019 17:01:51 -0300 (UYT)

Dear Parviz Seifpanahi Shabane,

The correct way to load a residue library is by using the command "loadoff"... Anyway, I suggest you to use the provided "cmd" files. If AMBER was correctly installed and the script "" was sourced, then there is no need for writing the full path to cmd files, this should be enough:

source leaprc.protein.ff14SB
source leaprc.DNA.bsc1

Some additional notes...

1) I'd use an octahedral box instead of a cubic one to save water and allowing molecular tumbling.

2) I'd first solvate the system and then use command "addIonsRand" to add ions. As nucleosome is a very charged complex then placing ions according to electrostatic potential may take a while, and may generate some issues due to PBC.

3) If you are adding salt to a high charged system, which it seem you are, then I'd take a look to this paper in order to do it right:

SLTCAP: A Simple Method for Calculating the Number of Ions Needed for MD Simulation []

4) I'd consider using NetCDF file format instead of ASCII (rst7, crd), which is lighter, more efficient and format free. This is particularly relevant for big systems which may escape restrictive file formats.



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Parviz Seifpanahi Shabane" <>
Para: "AMBER Mailing List" <>
Enviados: Viernes, 9 de Agosto 2019 13:54:06
Asunto: [AMBER] DNA force field.

Hi All,
I want to use FF99SB and parmBSC1 for my system. This my T-Leap script :
source /usr/local/amber18/dat/leap/lib/parmBSC1.lib
source /usr/local/amber18/dat/leap/cmd/oldff/leaprc.ff99SB

set default PBradii bondi
mods = loadAmberParams frcmod.opc
mods = loadAmberParams frcmod.ions1lm_126_iod_opc
mol = loadpdb 1kx5-HPP.pdb
addions mol Na+ 0
addions mol Cl- 0

solvateBox mol OPCBOX 25

addions2 mol Na+ 30
addions2 mol Cl- 30

saveamberparm mol 1KX5-ED25A-HPP-PDB-iodFF.crd
I am getting this error:
/usr/local/amber18/bin/teLeap: Fatal Error!
Error from the parser: syntax error
How can I solve this problem?
Parviz Seifpanahi
Ph.D. Candidate
Department of Physics
Virginia Tech, Blacksburg, Va 24061
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Received on Sat Aug 10 2019 - 13:30:02 PDT
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