AMBER: ptraj questions

From: Amber admin <>
Date: Sun, 31 Oct 2004 06:59:51 -0800

Dear users:
     I am using ptraj to calculate rmsd of one residue's sidechain by
fitting all the CAs. This is the input file:

reference ycd_rea.inpcrd
trajin md_nvt4.crd.gz
center .CA
image center
rms reference out rms-ycd-cry1-300k-mono1 :15-158.CA
rms reference out rms-ycd-rea-mono1-f114 :114.CG,CD1,CE1,CZ,CE2,CD2

The numbers I get are too small (around 0.05). The rmsd of CA is about
1.2. So I suppose the rmsd of this sidechain should be around this
number or larger.

Another problem I have is when I choose less than three atoms of the
sidechain, the program fails.

Thanks for your help in advance.

By the way, the ptraj program I have is ptraj-6.5.

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Received on Sun Oct 31 2004 - 15:53:00 PST
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