AMBER Archive (2009)

Subject: Re: [AMBER] DMF solvent box

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sun Sep 13 2009 - 04:25:33 CDT

Abhishek,

>     I search the database but no DMF molecule there. How can I get that.

Yes, this is normal: DMF is not yet available in R.E.DD.B.

Use R.E.D. http://q4md-forcefieldtools.org/RED/ to derive RESP charges
for DMF & please submit DMF in R.E.DD.B.

If you prefer I can do it for you, it is going to take 10 sec with R.E.D.
However, doing it by yourself would be a good exercice. Just let me know.

See Urea for another typical example (similar to what you need to do):
http://q4md-forcefieldtools.org/REDDB/projects/W-80/

regards, Francois

> --- 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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