Re: [AMBER] how to prepare a system with solvent of ethanol + water ?

From: vasu mathi <>
Date: Sat, 31 Jul 2010 22:27:31 +0530 (IST)

Hi wahyudi,
Thank you for the valuable help. I will proceed as you have suggested.


--- On Fri, 7/30/10, setyanto tri wahyudi <> wrote:

From: setyanto tri wahyudi <>
Subject: Re: [AMBER] how to prepare a system with solvent of ethanol + water ?
To: "AMBER Mailing List" <>
Date: Friday, July 30, 2010, 4:30 PM

Hello Vasu,.
You can use Packmol (, as
sugessted by david case.
With packmol you can add N number etanol and also N number of water.

This is my trick to use packmol :
 - use protein, etanol and water file PDB wtihout hidrogen, as you
 will got
H with LEAP.
 - you can use ethanol frcmod from amber or you can make with antechamber.
with antechamber, we got prep -file, continue with parmchk , we got

- You should know size of the box, so we can know the volume. So we can
predict how many water molekul if the box is full.

sincerely yours,

Setyanto Tri Wahyudi
Laboratorium Biokimia Komputasi
Program Studi Kimia
Sekolah Pascasarjana Kimia
Institut Teknologi Bandung

On Fri, Jul 30, 2010 at 5:06 PM, vasu mathi <> wrote:

>  Dear Amber,
> I want to do a simulation of a biomolecule in a mixed solvent of ethanol
> and water. Can anyone tell how do I go about this? From the previous amber
> mailing list I found that first I have to
 create an ethanol box and
> equilibrate it before solvating the biomolecule. I would appreciate if
> someone has done this already and provide the ethanol box library file. Also
> how do I prepare a system with a solvent of x% of ethanol + (1-x) % of water
> ?
> Thanks for any directions in advance.
> Regards,
> Vasu.
> _______________________________________________
> AMBER mailing list
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Received on Sat Jul 31 2010 - 10:00:03 PDT
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