AMBER Archive (2002)

Subject: RMSD calculation question

From: Soonmin Jang (sjang_at_protege.snu.ac.kr)
Date: Fri Oct 04 2002 - 02:02:37 CDT

Hi,

I am trying to calculate RMSd with amber trajectory "crd" file using
"carnal". (It is peptide with about 35 residues).
I need to calculate the RMSD for every crd time frame(about 1000 frames)
based on backbone(or CA atom).
The problem is that I need to compare with reference which is given
in "pdb" format. I know I can set reference for RMSd in "carnal" but
it seems it doesn't recognize pbd format.

How can I calculate RMSD with this ?

Here is my script with running results.
Thanks.

PS. I converted crd file into pdb file using VMD.
    I know 'VMD' can calculate RMSD also. Is there any method I can do in
    VMD ?

protege[3] 14> more rmsd.in
FILES_IN
  PARM p1 vii.parm;
STREAM s1
  md_200_rmsd.pdb;
STATIC ref_set viiu.pdb;
FILES_OUT
  TABLE tbl sm.rms;
DECLARE
  GROUP grp1 ( ATOM NAME CA );
  RMS fit1 FIT grp1 s1 ref_set;
OUTPUT
  TABLE tbl fit1 ;
END
protege[3] 15> carnal<rmsd.in

                          - CARNAL -
                          AMBER 6.0

                      COORDINATE ANALYSIS

input stdin
> FILES_IN
> PARM p1 vii.parm;
Reading parm file (vii.parm)
parm: opening vii.parm
> STREAM s1
> md_200_rmsd.pdb;
Using default parm (vii.parm) for STREAM s1
stream: opening md_200_rmsd.pdb
> STATIC ref_set viiu.pdb;
Using default parm vii.parm for STAT ref_set
stat: opening viiu.pdb
Error: viiu.pdb: full pdb format not supported
  Only ATOM records in amber order allowed
protege[3] 16>