AMBER Archive (2009)

Subject: Re: [AMBER] DMF solvent box

From: Abhishek Banerjee (a.banerjee_at_ymail.com)
Date: Mon Sep 14 2009 - 08:18:30 CDT

hi
    Thanks for your file.  Actually I was trying to use OPLSAA force field. I was wrong. Now with DMF and MEOH mol2 file I have created DMF.off and MEOH.off file with modified script1.ff. I created the solvant box with DMF. Then I edited what you told me to do. May be I editeded wrongly., atoms are not showing up in xLEAP. dmf_box.pdb is the modified pdb and dmf_box1.pdb is the original box. I am sending you the files. Plz check it. sorry for distrubing too much.
 
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>
Date: Sunday, 13 September, 2009, 5:01 PM

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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