AMBER Archive (2003)

Subject: Problem of Hbond in CARNAL

From: yuann (yuann_at_bioinfo.ndhu.edu.tw)
Date: Tue Apr 01 2003 - 06:08:59 CST

Daer AMBER users,
  I get an strange problem when I run CARNAL to get Hbond on my
system, which is okay for RMSd calculation by CARNAL. I also
take the top & crd file from 'polyA-polyT tutorial' to do Hbond
analysis, but CARNAL still returns the same message as follows,

------------------------------------------------------------------
                          - CARNAL -
                          AMBER 6.0

                      COORDINATE ANALYSIS

input stdin
> FILES_IN
> PARM p1 polyAT_vac.prmtop;
Reading parm file (polyAT_vac.prmtop)
parm: opening polyAT_vac.prmtop
> STREAM s1 polyAT_vac.inpcrd;
Using default parm (polyAT_vac.prmtop) for STREAM s1
stream: opening polyAT_vac.inpcrd
> FILES_OUT
> HBOND h1 h.bond TABLE LIST;
> DECLARE
> GROUP g1 (ATOM NAME H61 H62 H3);
** Group g1: 30 atoms
> GROUP g2 ((ATOM NAME O4)|((ATOM NAME N1)&(RES NAME DA DA5 DA3)));
** Group g2: 20 atoms
> OUTPUT
> HBOND h1 DONOR g1 ACCEPTOR g2 DISTANCE 3.3 STATS;
HBOND DONOR: no donor atoms in group
> END
STREAM s1: no more files/crds (iteration 1)
SUMMARY
--Hbond h1 stats:

Hbond_at_scorpio:[3]
---------------------------------------------------------------

Especially I've no idea why CARNAL says 'no donor atoms in group' even
though it has read the atoms specified in the groups before?
Thanks for your suggestion.

Best Regards,

sychen.