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

From: Babban Mia (babbanmia_at_gmail.com)
Date: Tue Aug 09 2011 - 09:42:26 CDT

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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