AMBER Archive (2009)
Subject: Re: [AMBER] DMF solvent box
From: Abhishek Banerjee (a.banerjee_at_ymail.com)
thanks a lot. I will try what u have suggested then get back to you.
--- On Sat, 12/9/09, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
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:
If you use the "Download projects" tool, you could look for projects about MeOH only as well:
- Then you solvate DMF (or MEOH as you prefer) by itself in LEaP
- 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:
- 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...
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