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

From: Ismail, Mohd F. (farid_at_ou.edu)
Date: Tue Aug 09 2011 - 13:02:19 CDT

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<mailto: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<mailto:owner-namd-l_at_ks.uiuc.edu> [owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>] on behalf of Babban Mia [babbanmia_at_gmail.com<mailto:babbanmia_at_gmail.com>]
Sent: Tuesday, August 09, 2011 1:20 AM
To: namd-l_at_ks.uiuc.edu<mailto: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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