AMBER Archive (2004)

Subject: AMBER: ptraj questions

From: Amber admin (amber-admin_at_scripps.edu)
Date: Sun Oct 31 2004 - 08:59:51 CST

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_at_CA
rms reference out rms-ycd-rea-mono1-f114 :114_at_CG,CD1,CE1,CZ,CE2,CD2
nofit

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.

Best,
Lishan
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu