AMBER Archive (2009)

Subject: Re: [AMBER] DMF solvent box

From: Abhishek Banerjee (a.banerjee_at_ymail.com)
Date: Sun Sep 13 2009 - 03:56:18 CDT

hi
    I search the database but no DMF molecule there. How can I get that.
Thanx
abhishek

--- On Sat, 12/9/09, FyD <fyd_at_q4md-forcefieldtools.org> wrote:

From: FyD <fyd_at_q4md-forcefieldtools.org>
Subject: Re: [AMBER] DMF solvent box
To: amber_at_ambermd.org
Date: Saturday, 12 September, 2009, 2:07 PM

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:
http://q4md-forcefieldtools.org/REDDB/projects/W-46/
 & its LEaP script:
http://q4md-forcefieldtools.org/REDDB/projects/W-46/script1.ff

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
See http://archive.ambermd.org/200405/0056.html
  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

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