AMBER Archive (2009)

Subject: Re: [AMBER] DMF solvent box

From: Abhishek Banerjee (a.banerjee_at_ymail.com)
Date: Sun Sep 13 2009 - 09:24:04 CDT

hi Francois
                       Thanks for your help. I have generated the mol2 for DMF and I used one paper for charges. But the problem is I have +0.394 extra charge on my molecule. How to handle this. I am sending you the paper and mol2 file.
Thanx
abhishek

--- On Sun, 13/9/09, FyD <fyd_at_q4md-forcefieldtools.org> wrote:

From: FyD <fyd_at_q4md-forcefieldtools.org>
Subject: Re: [AMBER] DMF solvent box
To: "AMBER Mailing List" <amber_at_ambermd.org>
Cc: q4md-fft_at_q4md-forcefieldtools.org
Date: Sunday, 13 September, 2009, 9:25 AM

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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