AMBER: Atom distance

From: <bybaker.itsa.ucsf.edu>
Date: Mon, 27 Sep 2004 6:59:05 +0000

Hello, Amber:

I would like to measure the distances between two atoms of my protein
model after the MD run. I use Carnal for the calculation. It did not go
through. From out-put file, it says no atom ND2 in residue 84. Last
token was O

I dont know what is wrong with my -Dist-input files. The ND2 atom is
shown in the original .pdb file. Why it can not be found. Then I change
the atom to other types, such as O, N, CA and so on, but the same
problems. They all can not be found. The program works fine if I just
want to measure the distance between two residues.

Please comment. I use Amber 7. The .prmtop and crd files are from MD run..

Thank you.

Bo


The input file:

Dist-1a.in

FILES_IN
  PARM p1 model1-3.prmtop;
  STREAM s1 model13md1.crd;
FILES_OUT
  TABLE t1 model13md11.dist;
DECLARE
  DIST d1 ND2 84 O 197;
OUTPUT
  TABLE t1 d1;
END


The output:

- CARNAL -
                          AMBER 4.1

                      COORDINATE ANALYSIS


input stdin
> FILES_IN
> PARM p1 model1-3.prmtop;
Reading parm file (model1-3.prmtop)
parm: opening model1-3.prmtop
                                                                                
> STREAM s1 model13md1.crd;
Using default parm (model1-3.prmtop) for STREAM s1
stream: opening model13md1.crd
> FILES_OUT
> TABLE t1 model13md11.dist;
> DECLARE
> DIST d1 ND2 84 O 197;
 -- no atom ND2 in residue 84 ---
DIST d1 ND2 84 O 197;
-------------- ^
   Error in stdin line 7. DIST: unexpected token
     Last token was O


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Received on Mon Sep 27 2004 - 08:53:00 PDT
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