From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Tue Aug 09 2011 - 13:29:52 CDT
Ismail, Baban,
You could easy assign charges by propka http://propka.ki.ku.dk/. Also
you could build your own EtOH/H2O cluster for solvation by Vega
http://nova.colombo58.unimi.it/cms/index.php?Software_projects:VEGA_ZZ
than you could use this cluster to solvate your peptide. Also you could
set -up and analyze NAMD calculations by the same program
Kind regards
On 8/9/2011 8:02 PM, Ismail, Mohd F. 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
> <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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