AMBER Archive (2009)

Subject: [AMBER] how can i deal with large number atoms

From: Wang,Ying (wangying_at_ufl.edu)
Date: Wed Feb 04 2009 - 23:04:23 CST

Hi, I simulate a system which have 10332 residues and I use the
pdb file to generate the top and crd files. Then I run the
simulation that have to fix the molecule in the heat process. I
use the commands as below:

Keep mole fixed with weak restraints
5.0
RES 1 10332
END
END

but when I use ambpdb command to regenerate pdb file from the top
and crd files I found that the number of residues can only up to
9999. after 9999 will start from 1 again. in this case, could I
still use the fix command as above? can amber recognize the
resides larger than 10000?
Thanks a lot! Your help will be greatly appreciated!

Best, 

--
Wang,Ying

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