AMBER Archive (2003)

Subject: Re: shake and H-O-H angle

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Tue Jan 21 2003 - 13:29:22 CST

Hi,
>
> I just realized that the angle term HW-OW-HW that appears in parm96 is
> not output to the parm/topol file when creating a simple water molecule
> with leap. I tried removing the bond H1-H2 of the TP3 water model, but
> still does not appear. Does anybody know how to make leap output this
> angle to the parm/topol file?
...I *believe* you could alter the code in ${WHATEVERPATH}/tleap/unit.c:
<snip>
zbUnitIgnoreAngle( STRING sA, STRING sB, STRING sC )
{

    if ( strcmp( sA, "OW" ) == 0 ) {
        if ( strcmp( sB, "HW" ) == 0 &&
             strcmp( sC, "HW" ) == 0 ) return(TRUE);
    }
    if ( strcmp( sB, "OW" ) == 0 ) {
        if ( strcmp( sA, "HW" ) == 0 &&
             strcmp( sC, "HW" ) == 0 ) return(TRUE);
    }
    if ( strcmp( sC, "OW" ) == 0 ) {
        if ( strcmp( sB, "HW" ) == 0 &&
             strcmp( sA, "HW" ) == 0 ) return(TRUE);
    }
<snip>
...and compile a special Leap-version that suits your needs.
Just give it a try (make the second TRUE a false).
Hope it helps
regards
Andreas

P.S.: I just tried it, it seems to work with NAMD, which doesn't like the
H-H bonds. Be sure to make some more thorough tests. 

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