AMBER Archive (2009)

Subject: Re: [AMBER] DMF solvent box

From: FyD (
Date: Sat Sep 12 2009 - 09:07:30 CDT

Dear Abhishek Banerjee,

> I have started MD simulation for a month back. I want to create a
> DMF and methanol mixture like binary mixture. Can some one give me
> some advice how to go about it. I am using amber 9

- You 1st need the charges & force field libraries (Tripos mol2 file
for instance) for the DMF & MeOH molecules taken individually.

To get the charges & Tripos mol2 files, you could look at the
R.E.DD.B. W-46 project:
  & its LEaP script:

If you use the "Download projects" tool, you could look for projects
about MeOH only as well:
Search... [Done]
Result(s) for search by Molecule name Methanol
Project name Methanol
Project code W-32
Project name Organic solvent
Project code W-46
Project name Organic solvent
Project code W-47
Project name Organic solvent
Project code W-48
Project name Organic solvent
Project code W-49

- Then you solvate DMF (or MEOH as you prefer) by itself in LEaP
   You save a PDB file for the DMF box created.

- For a 50/50 DMF/MeOH box, the idea is then to write a script to
modify in the PDB file the DMF molecules with an _even_ residue number:
   modify means :
* remove all atom of this DMF molecule but one: keep the oxygen for instance
* rename the oxygen name & residue name in agreement with the MeOH FF
library you previously built.

- You re-load in LEaP, the FF library (Tripos mol2 file) for DMF &
MeOH, then you load the PDB file of the modified DMF box. => LEaP will
add the missing atom for MeOH in the box.

You save the prmtop/prmcrd (build a frcmod file if required), you are
ready to equilibrate...

regards, Francois

AMBER mailing list