Hi,
There might be several other ways to do it but normally I do this way:
1) Open the complex in any molecular structure visaulization program (I use
PyMol for this) and delete the chain (in your case you can delete raf
chain) that you want to delete. For e.g in ras-raf.pdb, just delete the raf
chain and then gp to save..........molecule..............ras.pdb. DONE.
Repeat the same for raf.pdb.
2) Other way I do is using this command along the command line: awk
'NR>=starting line number for first protein && NR<=ending line number '
ras,raf.pdb > ras.pdb
This will create a separate PDB named ras.pdb with residues you mentioned.
Please note that here you need to use line number and NOT the residue
number. When you view your ras-raf complex (vi ras-raf.pdb) at the very
bottom right corner you can see line number. So note the starting and
ending line number for the atoms for each chain and use accordingly after
NR.
I hope this helps
On Sun, Feb 28, 2016 at 2:39 AM, Mahdieh Hadi <mahdieh.hadi.bric.ku.dk>
wrote:
> Hi,
> Excuse me, I have a real basic question. I am going through the tutorial 3.
>
> http://ambermd.org/tutorials/advanced/tutorial3/section1.htm
>
> and I do not know how could I prepare ras.pdb and raf.pdb from the
> ras-raf.pdb complex?
>
> I really appreciate if you could help me,
> Bests
> Mahdieh
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>
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Received on Sun Feb 28 2016 - 05:00:03 PST
