Justin Lemkul писал 07-11-2012 16:20:
On 11/7/12 7:10 AM, Steven Neumann wrote:
On Wed, Nov 7, 2012 at 11:56 AM, Justin Lemkul jalem...@vt.edu
wrote:
On 11/7/12 4:19 AM, Steven Neumann wrote:
Dear Gmx Users,
I am trying to simulate protein-ligand interactions at specific
pH=5.
I
Hi,
Do you mean the pKa value of the side chain in solution? Or the pKa value
in ethanol, DMSO, hexane? Maybe the pKa value in a membrane, or in the
interior of a protein, perhaps in a hydrophobic pocket? Or the pKa with
one/two/three neighbouring acidic/basic residues? If you have literature
On 11/7/12 4:19 AM, Steven Neumann wrote:
Dear Gmx Users,
I am trying to simulate protein-ligand interactions at specific pH=5.
I processed my protein.pdb into the H++. As I see from th titration
curve of the entire molecule it appears that at pH=5 the total charge
should be equal to 2. When
On Wed, Nov 7, 2012 at 11:56 AM, Justin Lemkul jalem...@vt.edu wrote:
On 11/7/12 4:19 AM, Steven Neumann wrote:
Dear Gmx Users,
I am trying to simulate protein-ligand interactions at specific pH=5.
I processed my protein.pdb into the H++. As I see from th titration
curve of the entire
On 11/7/12 7:10 AM, Steven Neumann wrote:
On Wed, Nov 7, 2012 at 11:56 AM, Justin Lemkul jalem...@vt.edu wrote:
On 11/7/12 4:19 AM, Steven Neumann wrote:
Dear Gmx Users,
I am trying to simulate protein-ligand interactions at specific pH=5.
I processed my protein.pdb into the H++. As I
On Wed, Nov 7, 2012 at 12:20 PM, Justin Lemkul jalem...@vt.edu wrote:
On 11/7/12 7:10 AM, Steven Neumann wrote:
On Wed, Nov 7, 2012 at 11:56 AM, Justin Lemkul jalem...@vt.edu wrote:
On 11/7/12 4:19 AM, Steven Neumann wrote:
Dear Gmx Users,
I am trying to simulate protein-ligand
Hi,
I've used the H++ server myself at times. My experience is that it's rather
sensitive to the very fine detail of the input structure in some cases. I've
had situations where H++ suggest one protonation state, then a short md
simulation takes the system to a slightly different conformation
On Wed, Nov 7, 2012 at 2:55 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
Hi,
I've used the H++ server myself at times. My experience is that it's rather
sensitive to the very fine detail of the input structure in some cases. I've
had situations where H++ suggest one protonation state, then
7 nov 2012 kl. 16.21 skrev Steven Neumann:
On Wed, Nov 7, 2012 at 2:55 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
Hi,
I've used the H++ server myself at times. My experience is that it's rather
sensitive to the very fine detail of the input structure in some cases. I've
had
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