Hi,
You can use cpptraj to manipulate PDB files like this. If you load the
PDB using cpptraj you can see it has 4 molecules:
$ cpptraj
> parm ras-raf.pdb
> molinfo
#Mol Natom #Res Name
1 2621 1 MET
2 1241 167 ASN
3 44 243 GTP
4 1 244 MG
This tells you what residue ranges correspond to which molecules. To
generate RAS, you can then load the RAS-RAF PDB and strip away
everything but RAS:
> loadcrd ras-raf.pdb name RAS
> crdaction RAS strip !:1-166
> crdout RAS RAS.pdb
Then repeat for RAF:
> loadcrd ras-raf.pdb name RAF
> crdaction RAF strip !:167-242
> crdout RAF RAF.pdb
All of these commands can be put into a single script. Hope this helps,
-Dan
On Sun, Feb 28, 2016 at 12:39 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Sun Feb 28 2016 - 06:00:05 PST
