AMBER Archive (2003)

Subject: question about H-bond in carnal?

From: Lishan Yao (yaolisha_at_msu.edu)
Date: Fri Apr 25 2003 - 09:44:55 CDT

Hi there:
    I used carnal to calculate H-bond between ligands and protein,
ligands and water. This is output file I got. It complains about the
atoms in ligands. What should I do? Please help.

Sincerely
Lishan

input hbond
Reading parm file (dhna_mnp.prmtop)
parm: opening dhna_mnp.prmtop
> # HBOND ANALYSIS EXAMPLE
> FILES_IN
> PARM p1 dhna_mnp.prmtop;
Reading parm file (dhna_mnp.prmtop)
parm: opening dhna_mnp.prmtop
> STREAM s1 md_nvt3.crd md_nvt4.crd;
Using default parm (dhna_mnp.prmtop) for STREAM s1
 (box will be read from stream)
stream: opening md_nvt4.crd
stream: opening md_nvt3.crd
> FILES_OUT
> HBOND h1 xhb1 TABLE LIST;
> HBOND h2 xhb2 TABLE LIST;
> HBOND h3 xhb3 TABLE LIST;
> HBOND h4 xhb4 TABLE LIST;
> DECLARE
> GROUP g1 ((RES 969,970,971,973)&(ATOM TYPE n? o?));
** Group g1: 36 atoms
> GROUP g2 ((RES 1-968)&(ATOM TYPE N? O?));
** Group g2: 2840 atoms
> GROUP g3 (ATOM TYPE OW);
** Group g3: 24534 atoms
> OUTPUT
> HBOND h1 DONOR g1 ACCEPTOR g2 DISTANCE 3.3 ANGLE 45.0 STATS;
HBOND DONOR: no donor atoms in group
> HBOND h2 DONOR g2 ACCEPTOR g1 DISTANCE 3.3 ANGLE 45.0 STATS;
HBOND ACCEPTOR: no acceptor atoms in group
> HBOND h3 DONOR g1 ACCEPTOR g3 DISTANCE 4.5 ANGLE 60.0 STATS;
HBOND DONOR: no donor atoms in group
> HBOND h4 DONOR g3 ACCEPTOR g1 DISTANCE 4.5 ANGLE 60.0 STATS;
HBOND ACCEPTOR: no acceptor atoms in group
> END