Hello,
I was hoping someone might be able to set me in the right direction as to a
query I had regarding amber 10.
I've run a long MD simulation with explicit waters of a ligand bound to a
protein. I would like to identify which protein residues make contact with
the ligand, so that I know what residues to look at in a per-residue
decomposition.
I've been playing with the contacts command in ptraj. In the results, I get
two columns: example:
######################
#time residue 157
1.00 663
2.00 663
3.00 663
4.00 643
5.00 663
6.00 663
7.00 683
8.00 663
9.00 683
11.00 643
12.00 683
13.00 643
14.00 663
15.00 683
16.00 683
#####################
I take it that the first column is the snapshot number, whilst the second is
the total number of contacts between atoms specified in my mask for that
snapshot/frame. I am confused about why it says residue 157 at the top. My
protein has 157 residues, but my ligand (specified in the mask) occupies
position 158. Is this because res 157 is the last residue that uses standard
amber atom types or something?
Additionally, is there a better way for me to identify which residue numbers
contact the ligand apart from running the command for every protein residue
with the ligand? e.g
mask = ligand +residue1
mask = ligand +residue2
mask = ligand +residue3
etc...
I would be grateful for any comments you might have.
Best regards,
GT
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Received on Wed May 11 2011 - 09:30:03 PDT
