AMBER Archive (2004)

Subject: AMBER: Treating atom type LP the same as EP

From: Sarah Wittkopp (tschampe_at_sunchem.chem.uga.edu)
Date: Mon May 17 2004 - 14:16:20 CDT

Hi,

I am hoping to have the atom type LP treated analytically as the EP is in
MD simulations. Therefore, the code has to be modified in both leap and
sander. As a non-programmer, from what I can see the three important
files will be unit.c unitio.c and extra_pts.f. I have attempted to modify
the unitio.c file as follows:

old (line 4333)
    /*NUMEXTRA*/
    iNumExtra = 0;
    for ( i=0; i<iVarArrayElementCount(uUnit->vaAtoms); i++ ) {
                cPTemp = sAtomType( PVAI(uUnit->vaAtoms, SAVEATOMt, i
)->aAtom );
                if( !strncmp( cPTemp, "EP", 2 )) iNumExtra++;
    }
    FortranWriteInt( iNumExtra );

modified
    /*NUMEXTRA*/
    iNumExtra = 0;
    for ( i=0; i<iVarArrayElementCount(uUnit->vaAtoms); i++ ) {
                cPTemp = sAtomType( PVAI(uUnit->vaAtoms, SAVEATOMt, i
)->aAtom );
                if( !strncmp( cPTemp, "EP", 2 ) || !strncmp( cPTemp, "LP",
2 ) ) iNumExtra++;
    }
    FortranWriteInt( iNumExtra );

I have then modified other occurances in unit.c and unitio.c in the same
fashion, but the value from NEXTRA still only includes EPs, but not LPs.
I want to be able to have different oxygen - extra point and oxygen lone
pair distances to investigate the effects that lone pairs have. Any
thoughts or ideas would be greatly appreciated.

Cheers,
Sarah

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