[AMBER] tLeap and acetonitrile/chloroform solvation

From: Luka Bilić <Luka.Bilic.irb.hr>
Date: Wed, 04 Jan 2017 15:12:51 +0100

To whom it may concern,

I am writing to enquire about solvation of organic molecules in Amber 16.
So far I've had some troubles in navigating tutorials and manual in
regards to solvating a molecule in acetonitrile or chloroform. So this
e-mail will contain 2 questions/problems with similar content.

1st question/problem:
I've found that the Amber 16 has "solvents.lib" and appropriate frcmod
file for chloroform, but I am not sure how to use this to solvate my
molecule of interest with this. My molecule of interest is a .log file
from Gaussian optimisation. I have used antechamber to change it in
.mol2 file type so I can work with it in Amber 16. Now I will present
an input feed so you may see where Currently I'm unable to continue
without help or advice but I will try to understand this on my own in
the meantime.

-I: Adding /home/user/amber16/dat/leap/prep to search path. -I: Adding
/home/user/amber16/dat/leap/lib to search path.
-I: Adding /home/user/amber16/dat/leap/parm to search path.
-I: Adding /home/user/amber16/dat/leap/cmd to search path.

Welcome to LEaP!
(no leaprc in search path)
source leaprc.gaff2
----- Source: /home/user/amber16/dat/leap/cmd/leaprc.gaff2 -----
Source of /home/user/amber16/dat/leap/cmd/leaprc.gaff2 done
Log file: ./leap.log
Loading parameters: /home/user/amber16/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.1, April 2016)
loadamberparams frcmod.chcl3
Loading parameters: /home/user/amber16/dat/leap/parm/frcmod.chcl3
Reading force field modification type file (frcmod)
Reading title:
  chloroform frcmod file

So the next obvious step would be to define what my molecule of
interest is by adding line

"molecule=loadmol2 MoleculeOfInterest.mol2"

And from this spot troubles arise.

How do I use "solvateoct molecule Solvent 14.0" correctly?
Do I have to have chloroform structure minimized (in Gaussian for
instance) and then turned into .mol2 file, after which I load it in
tLeap using "Solvent=loadmol2 Solvent.mol2" or do I have to do
something else?

2nd question/problem
Since I have found no acetonitrile .lib files. How do I make a solvent
box containing well defined .frcmod and .lib files. My current .frcmod
files made from Acetonitrile.mol2 all end up empty.

remark goes here





In other words, (how) can I make my own explicit acetonitrile
parameters for solvation of organic molecules in order to do MD
simulations. This question may be generalized to: How do I make custom
solvent parameters and how do I use them for explicit solvation of
molecules (organic molecules, metal complex compounds and proteins).

If this all seems trivial to someone, please understand that this is
the 5th day of my life where I'm trying to do something in Amber. I do
not want to go blindly through tutorials because that will give me
false sense of knowledge and skills (both of which will take months,
if not years to properly acquire).

Also thank you for your understanding and help.

Yours Luka

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Received on Wed Jan 04 2017 - 06:30:03 PST
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