AMBER Archive (2007)

Subject: Re: AMBER: Problem in running CARNAL

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Fri Dec 07 2007 - 11:48:15 CST

 FILES_OUT
    HBOND h1 xhb TABLE LIST;
    HBOND h2 xhb TABLE LIST;
    HBOND h3 xhb TABLE LIST;
    ...

You are defining multiple files with the same name (xhb.*).
One thing you might consider is to define one set of xhb files
(xhb.tab, xhb.lis I think) and direct multiple hbonds to be
reported there, by specifying a single donor group and a single
acceptor group. Alternatively you could create lots of output
files in which case you need to give a different name for each
(xhb1, xhb2..).

I see your RES 1 has lots of oxygens, and you have also defined
multiple groups on the same ones, which isn't necessary:

            GROUP g1 ((ATOM NAME O12) & ( RES 1));
            GROUP g14 ((ATOM NAME O12) & ( RES 1));
            GROUP g25 ((ATOM NAME O12) & ( RES 1));
            GROUP g36 ((ATOM NAME O12) & ( RES 1));
            GROUP g47 ((ATOM NAME O12) & ( RES 1));
            GROUP g58 ((ATOM NAME O12) & ( RES 1));
            GROUP g69 ((ATOM NAME O12) & ( RES 1));

(Once a group is defined, it can be used multiple times.)

If you want intra-res1 hbonds, the simple thing may be to define
a single group, RES 1, and give it as donor and acceptor:

 FILES_OUT
    HBOND h1 xhb TABLE LIST;
 DECLARE
    GROUP g1 (RES 1);
 OUTPUT
    HBOND h1 DONOR g1 ACCEPTOR g1 DISTANCE 4.0 ANGLE 60.0 STATS;

(Note the spelling of ACCEPTOR.) This might work ok too:

    HBOND h1 g1 STATS;

Bill
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