AMBER Archive (2004)

Subject: AMBER: alignment problem using carnal

From: xhu1_at_memphis.edu
Date: Thu Mar 18 2004 - 13:48:55 CST

Dear Ambers,

I am using carnal to align the CAs in each snapshot to the start
structure. But the coordinates i got are far away from the start
structure. Even I align the start structure self, the results are
totally different. For example:

at the start structure, the first CA, before alignment:

ATOM 13 CA PRO 1 49.307 54.792 42.016

after alignment:

ATOM 1 CA PRO 1 13.987 12.578 1.321

at the first snapshot, the first CA, after alignment:

ATOM 1 CA PRO 1 13.169 14.360 0.580

Is it reasonable for carnal, or something I missed in my input file?
Any comments are very welcome. Thank you so much!

All the best

Shawn

PS. My input file as following:

FILES_IN
  PARM p1 pp.parm;
  STREAM s1 d4phvMD_pp.trj;
  STATIC st1 pp.crd;
FILES_OUT
  COORD crd1 d4phv_align_CA.crd APPEND CRD;
DECLARE
  GROUP g1 ((RES 1 - 198) & (ATOM NAME CA));
  RMS r1 FIT g1 s1 st1;
OUTPUT
  COORD crd1 r1 GROUP g1;
END

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