Re: Explicit Solvent Sytem (40% Ethanol + 60% Water)

From: Babban Mia (babbanmia_at_gmail.com)
Date: Wed Aug 10 2011 - 04:49:20 CDT

Hello Dr. Ismail

Thanks for the information.
I did as you suggested but now I am having some trouble relating to the
parameters and topology file for my PACKMOL created PDB file.
The entries in which look something like this :

Where HOH is water molecule and LIG is ethanol.
I need to create a PSF file for this PDB which then can be further used in
NAMD and all and I do not know how to appropriately do that.

Can you please advise on how and which topology/parameter file I should use
to generate the PSF for the PDB which looks like below:
How do you use two different topology/parameter file to generate psf using
psfgen as you mentioned there might me different parameters/toplogy for
water and ethanol separately.

HETATM 1796 H HOH A9999 25.464 1.713 38.349 1.00 0.00
H
HETATM 1797 H HOH A9999 24.396 0.630 38.482 1.00 0.00
H
HETATM 1798 O HOH A 1 27.837 27.741 20.582 1.00 0.00
O
HETATM 1799 H HOH A9999 28.682 28.113 20.289 1.00 0.00
H
HETATM 1800 H HOH A9999 27.555 28.333 21.296 1.00 0.00
H
HETATM 1801 C LIG B 1 31.896 22.058 1.874 1.00 0.00
C
HETATM 1802 C LIG B 1 31.274 23.418 2.110 1.00 0.00
C
HETATM 1803 H LIG B 1 32.875 22.160 1.393 1.00 0.00
H
HETATM 1804 H LIG B 1 31.254 21.439 1.242 1.00 0.00
H
HETATM 1805 H LIG B 1 32.063 21.540 2.825 1.00 0.00
H

Please advise.

Best
Babban

On Tue, Aug 9, 2011 at 11:32 PM, Ismail, Mohd F. <farid_at_ou.edu> wrote:

> Use Packmol to create your pdb file - google packmol. You'll need your
> protein pdb file, pdb file of one copy of water, and pdb file of one copy of
> ethanol, you can create this easily with avogadro for example. Use packmol
> to create a pdb file of the combination of them all.
>
> Get the topology file from Prof. Mackerell website for your protein (and
> maybe water), and from cgenff for ethanol.
>
> Use those two to create the psf file using psfgen. Google how to create
> psf file from namd.
>
> HTH,
> Farid Ismail
>
> ------------------------------
> *From:* Babban Mia [babbanmia_at_gmail.com]
> *Sent:* Tuesday, August 09, 2011 9:42 AM
> *To:* Ismail, Mohd F.; namd-l_at_ks.uiuc.edu
> *Subject:* Re: namd-l: Explicit Solvent Sytem (40% Ethanol + 60% Water)
>
> Thanks a lot Ismail
> But my main problem is setting up the explicit system.
> I don't have access to charmm anymore
> How should I use VMD/NAMD to solvate the protein with (40% Ethanol+ 60%
> Water) ?
> Once I solvate it ,I could save the pdb and psf file for the MD run
>
> Thanks again but more info would be great
>
> Best
> Babban
>
> On Tue, Aug 9, 2011 at 8:04 PM, Ismail, Mohd F. <farid_at_ou.edu> wrote:
>
>> You can "transfer" your system from charmm to NAMD by creating a psf and
>> a pdb file from charmm. That's all NAMD needs.
>>
>> I don't know much about the ability to change pH in NAMD nor charmm.
>>
>> HTH,
>> Farid Ismail
>> Graduate Student
>> Dept. of Chemistry/Biochemistry
>> University of Oklahoma
>>
>> ------------------------------
>> *From:* owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of
>> Babban Mia [babbanmia_at_gmail.com]
>> *Sent:* Tuesday, August 09, 2011 1:20 AM
>> *To:* namd-l_at_ks.uiuc.edu
>> *Subject:* namd-l: Explicit Solvent Sytem (40% Ethanol + 60% Water)
>>
>> Hello NAMD users
>>
>> My name is Babban and I have just started to use NAMD and I had been using
>> CHARMM for a long time before that.
>>
>> I have following queries regarding an MD simulation that I want to set up
>> ?
>>
>> 1. I want to do a MD in Periodic Boundary Condition for my peptide which
>> is like 350 amino acids in a combined Ethanol+Water System where Ethanol
>> would be 40%
>> Can somebody explain me in good detail about doing that ?
>>
>> 2. Is there way one change/set pH in NAMD ?. I did not find such a thing
>> in the tutorials?
>>
>> 3. At a pH of 7.4 ,my peptide will have some charge and I would need to
>> put equivalent charge in my PDB unit cell to neutralize the system?. Those
>> charges are to be put in local minima.
>> How do I achieve that?
>>
>>
>> Please advise.
>>
>> In anticipation of an encouraigng reply
>>
>> Best regards
>> Babban
>> UBC
>>
>>
>>
>

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