Try to use ptraj distributed with Amber 7. For me it seems much more flexile than carnal.
Tomas
On Mon, Sep 27, 2004 at 06:59:05AM +0000, bybaker.itsa.ucsf.edu wrote:
> 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;
> --? 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
