Hi,
I want to make an index file for a certain residue, say residue 14 and its
atom CA. I can eaily do that if its a single chain protein, but my protein
contains 10 chains and I don't know how to select residue 14 from each
chain. I tried splitting the protein into chains by using splitch
Hi,
As an example, assuming that I have four chains (A,B,C,D) and want to
select residue 14 in chains A,B and D
1 r 14 chain A|1 r 14 chain B| 1 r 14 chain D
1 is usually the default group 'protein'. If that is not so in your case,
substitute it with the appropriate number. I think 3 is
Thank you for your response. But in the gro file there are no names for
chains in mdrun.gro file. Moreover, if I am selecting only CA of residue 14
for chain A using the following command, I get 10 atoms, but I should get
only 1 atom.
r 14 a CA chain A.
It means that the tool is taking CA of
Hello,
Can you index your residues so that each residue gets a unique number.
pdb2gmx has an option -renum that will do this for you.
Best,
Eric
On Tue, Nov 4, 2014 at 10:33 PM, bharat gupta bharat.85.m...@gmail.com
wrote:
Thank you for your response. But in the gro file there are no names
But is it necessary to renumber the residues .. Can this be done in some
other way
On Wed, Nov 5, 2014 at 2:49 PM, Eric Smoll ericsm...@gmail.com wrote:
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Hi,
If you are going to work with multiple chains, create a .tpr with a pdb
file of your system that specifies the protein chains for analysis.
Here is how I would do it. Take the initial .gro configuration of your MD
run, convert it into pdb using editconf. Assign chain identifiers to the
