Re: [AMBER] tLeap and acetonitrile/chloroform solvation

From: Luka Bilić <>
Date: Thu, 05 Jan 2017 09:17:51 +0100

Thank you for your reply.

By using information from your reply (with some trial and error) I was
able to get to the point I desired. Since I'm used to using programs
with complete GUI Amber is quite a joyful challenge.

I realised what was the problem when I was making .frcmod files. It's
not trivial to create .mol2 file from Gaussian09 .log file. Openbabel
software provided me with a proper .mol2 file. In other words I
converted Gaussian09 .log file into .mol2 using Openbabel and this in
return gave me complete .mol2 file from which I was able to make
non-empty .frcmod file.
For now this is not so important, Gaff2 has everything I currently
need. However later when (if?) I will be doing some things in unusual
solvents I might need to play with some solvent parameters.

Anyway, thank you for pointing me in the right direction!
I hope I will be able to return to favor one day.

Yours Luka

Citiram Huang Jing <>:

> Here is a tutorial to have a typical molecular dynamics; you could follow
> the procedures in this tuturial and then it would be easy to manage your
> own molecules;
> 1st question:
> Following is the command in the manual;
>> mol = loadpdb my.pdb
>> solvateOct mol TIP3PBOX 12.0 0.75
> 2nd question:
> Use "antechamber" to creat the .mol2 and .frcmod for the non-library
> molecules;
> jing
> On Wed, Jan 4, 2017 at 4:12 PM, Luka Bilić <> wrote:
>> 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.
>> "
>> tleap
>> -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.
>> .frcmod
>> "
>> 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
>> _______________________________________________
>> AMBER mailing list
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Thu Jan 05 2017 - 00:30:04 PST
Custom Search