AMBER Archive (2009)

Subject: RE: [AMBER] Xleap - solvatebox - counterions

From: amirhossein taghavi (amirhosseintaghavi786_at_hotmail.com)
Date: Sat Jan 31 2009 - 11:34:10 CST

Dear Sir
 
I think this could be help:
 
A comparative study of the hydration of Na+ and K+ with refined
polarizable model potentials. journal of chemical physics/118(15)/p.7062
 
amir
> Date: Fri, 30 Jan 2009 11:04:23 -0500> From: case_at_biomaps.rutgers.edu> To: arnaud_at_lcc-toulouse.fr; amber_at_ambermd.org> Subject: Re: [AMBER] Xleap - solvatebox - counterions> CC: > > On Fri, Jan 30, 2009, Arnaud wrote:> > > I use xleap on amber10 package and I am quite surprise by some results.> > If I solvate (solvatebox test TIP3PBOX 10) my molecular system previously> > neutralized with Na+ counterions (addions test Na+ 0) the number of water> > residues added is 5824.> > If I solvate the same molecular system previously neutralized with K+, the> > number of water residues increase to 7846. > > > > With xleap on amber9 package, these values are different respectively 4674> > and 5183.> > I don't have an answer to your question, but I think it is generally> preferable to use solvateBox first, then use addIons to replace some of> the solvent water molecules with ions. Maybe Tom Cheatham or Wei Zhang> have some good ideas here.> > Also, you can try the following patch to> $AMBERHOME/src/leap/src/commands.c.
This is in the current CVS tree,> but doesn't seem to be in the bugfixes for Amber10. But I'm not sure if> this is related or not.> > Or, try sleap instead of leap.> > ...regards...dac> > Index: commands.c> ===================================================================> RCS file: /home/amber_cvs/cvsroot/amber11/src/leap/src/leap/commands.c,v> retrieving revision 10.0> retrieving revision 10.1> diff -c -r10.0 -r10.1> *** commands.c 15 Apr 2008 23:22:21 -0000 10.0> --- commands.c 16 Jul 2008 20:14:46 -0000 10.1> ***************> *** 5144,5151 ****> AtomSetFlags( aAtom, ATOMPOSITIONKNOWN );> }> dMinSize = dIonSize1;> if ( uIon2 ) {> - dIonSize2 = 0.0;> iUnknown = 0;> lAtoms = lLoop( (OBJEKT)uIon2, ATOMS );> for(i=0; aAtom = (ATOM)oNext(&lAtoms); i++) {> --- 5144,5151 ----> AtomSetFlags( aAtom, ATOMPOSITIONKNOWN );> }> dMinSize = dIonSize1;> + dIonSize2 = 0.0;> if ( uIon2 ) {> iUnknown = 0;> lAtoms = lLoop( (OBJEKT)uIon2, ATOMS );> for(i=0; aAtom = (ATOM)oNext(&lAtoms); i++) {> ***************> *** 5181,518
6 ****> --- 5181,5193 ----> VP0(( "Adding %d counter ions to \"%s\" using 1A grid\n", > iIon1 + iIon2, sAssocName( aaArgs[0] )));> > + if (iIon1 + iIon2 > 5) {> + const double xx = (double) (iIon1 + iIon2);> + const double ff = exp(log(xx + 1.0)/3.0);> + dMinSize = (dIonSize1 > dIonSize2 ? dIonSize1 : dIonSize2);> + dMinSize *= (ff > 1.0 ? ff : 1.0);> + }> + > if ( iIon1 + iIon2 == 0 )> return(NULL);> > ***************> *** 6253,6259 ****> lAtoms = lLoop((OBJEKT) uUnit, ATOMS );> while ( aAtom = (ATOM)oNext(&lAtoms) ) {> if ( bAtomFlagsSet( aAtom, ATOMSELECTED ) ) {> ! bBuildFlipChiralityFor( uUnit, aAtom );> }> }> > --- 6260,6266 ----> lAtoms = lLoop((OBJEKT) uUnit, ATOMS );> while ( aAtom = (ATOM)oNext(&lAtoms) ) {> if ( bAtomFlagsSet( aAtom, ATOMSELECTED ) ) {> ! bBuildFlipChiralityFor((CONTAINER) uUnit, aAtom );> }> }> > > _______________________________________________> AMBER mailing list> AMBER_at_ambermd.org> http://lists.ambermd.org/mailman/listinfo/amber
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