AMBER Archive (2009)

Subject: [AMBER] question with hbond in carnal

From: Ganesh Kamath (gkamath9173_at_gmail.com)
Date: Tue Oct 20 2009 - 08:58:36 CDT

Hi,

 I am trying to find the number/occupancy of hbonds near a carboxylic
group O which is tail of substrate with the
waters surrounding it. I tried using ptraj with hbond keyword which
gives me a segmentation fault.
Now I am trying to use hbond with carnal
My input script is

FILES_IN
PARM p1 r6p.top;
STREAM s1 0.00.crd;

FILES_OUT
HBOND h1 xhb TABLE LIST;

DECLARE
GROUP g1 ((RES 233)&(ATOM TYPE OE1));
GROUP g2 (ATOM TYPE H1 H2) ;

OUTPUT
HBOND h1 DONOR EXACT g1 ACCEPTOR EXACT g2 STATS;
END

I get this message that there are no donor or acceptor atoms and the
xhb.list and tab does not contain anything.
My atom type is OE1 for the carboxylic oxygen. It first doesnt
recognize the atom name so I change to O and then
I get this.

HBOND DONOR: no donor atoms in group
HBOND ACCEPTOR: no acceptor atoms in group

Could you please help me.

thanks,

ganesh

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