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;
http://ambermd.org/tutorials/basic/tutorial0/
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;
http://ambermd.org/tutorials/basic/tutorial4b/
jing
On Wed, Jan 4, 2017 at 4:12 PM, Luka Bilić <Luka.Bilic.irb.hr> 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
> MASS
>
> BOND
>
> ANGLE
>
> DIHE
>
> IMPROPER
>
> NONBON
> "
> 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.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jan 04 2017 - 08:00:02 PST
