AMBER Archive (2009)

Subject: Re: [AMBER] DMF solvent box

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sun Sep 13 2009 - 12:01:13 CDT

Dear Abhishek,

>                        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.

I have no idea how you got these charges: For sure, +0.394 is wrong...

See http://q4md-forcefieldtools.org/FyD/DMF/ to get the corresponding
R.E.D. run:

http://q4md-forcefieldtools.org/FyD/DMF/Ante_RED/
   => Ante_R.E.D. execution & Gaussian 2009 geometry optimization

http://q4md-forcefieldtools.org/FyD/DMF/Data-RED/
   => R.E.D. run

The R.E.D. log file:
http://q4md-forcefieldtools.org/FyD/DMF/RED-vIII.3.log

The RESP inputs:
http://q4md-forcefieldtools.org/FyD/DMF/Data-RED/input1_m1
http://q4md-forcefieldtools.org/FyD/DMF/Data-RED/input1_m1

  & the RESP charges within the Tripos mol2 file:
http://q4md-forcefieldtools.org/FyD/DMF/Data-RED/Mol_m1-o1.mol2
    => Total charge = 0.0000

Your file is @
http://q4md-forcefieldtools.org/FyD/DMF/dmf.mol2

  --

http://q4md-forcefieldtools.org/FyD/DMF/Data-RED/Mol_m1-o1.mol2
  &
http://q4md-forcefieldtools.org/FyD/DMF/dmf.mol2
are quite different...

I did a very quick job... However, the total charge = 0.

regards, Francois

> --- 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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