Dear users,
Kindly clarify my doubt regarding salt bridge calculation.
Thank you
Regards
Kavya
On Mon, Apr 1, 2013 at 3:48 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
For calculating salt bridge in proteins I
am using g_hbond instead of g_saltbr.
In g_hbond I use contact and
You can use g_dist with specific atoms indices to calculate distances,
if you already have the information about atoms involved in salt
bridge interactions.
On Tue, Apr 2, 2013 at 5:10 PM, Kavyashree M hmkv...@gmail.com wrote:
Dear users,
Kindly clarify my doubt regarding salt bridge
Sir,
Thank you very much for your reply. I wanted to calculate
Salt bridge in the whole protein so i am not mentioning the
residues involved. The problem with g_saltbr was that if I
have to calculate the accessibility of these atoms it will be
a problem because it gives the charge groups but not
On 4/2/13 11:58 AM, Kavyashree M wrote:
Sir,
Thank you very much for your reply. I wanted to calculate
Salt bridge in the whole protein so i am not mentioning the
residues involved. The problem with g_saltbr was that if I
have to calculate the accessibility of these atoms it will be
a problem
Sir,
This g_hbond will generate a matrix similar to
what g_saltbr would have given in terms of variation
of distance between two charge groups.
I want to find out the variation of all the salt bridges
in the protein over the trajectory, if I have to use g_dist
with an index of positive atoms and
On Tue, Apr 2, 2013 at 1:09 PM, Kavyashree M hmkv...@gmail.com wrote:
Sir,
This g_hbond will generate a matrix similar to
what g_saltbr would have given in terms of variation
of distance between two charge groups.
I suppose, in that sense, the output can be useful.
I want to find out
Sir,
Thank you for the detailed insight. As you mentioned
It does not give much information. But the matrix that
it would generate would only show whether a specific
salt bridge (SB) exited at a given time within the cut-off (0.4).
I got your explanation. Yes water mediated SBs are also
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