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 don’t 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;
--à no atom ND2 in residue 84 ß---
DIST d1 ND2’ 84 O’ 197;
-------------- ^
Error in stdin line 7. DIST: unexpected token
Last token was O’
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Sep 27 2004 - 08:53:00 PDT
