Hi amber users,
I know this question has been posted on the amber list a while ago.
It seems that amber-NAMD compatibility for water is dependent on having in
the prmtop file the angles printed out.
The suggestion was to modify the unit.c file as below:
> 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(FALSE); !!!!!!!
> }
> if ( strcmp( sC, "OW" ) == 0 ) {
> if ( strcmp( sB, "HW" ) == 0 &&
> strcmp( sA, "HW" ) == 0 ) return(TRUE);
> }
>
> /* delete all angles related to extra points */
> if( GDefaults.iDeleteExtraPointAngles ){
> if ( strcmp( sA, "EP" ) == 0 || strcmp( sC, "EP" ) == 0 ) return(TRUE);
> }
>
> return(FALSE);
> }
I've recompiled tleap using the command in the Makefile
cd leap/src/leap; make -f Makefile.tleap install
I've tried to recompile xleap as well
cd leap; xmkmf
cd leap; make World
cd leap; make install.leap
and I've even tried recompiling the whole amber package.
I've also tried to replace the "OW" and "HW" strings in the routine above
with some strings that do not exist, e.g. "Rn" and "Eu".
However when I generate a new file with only water I do not see any
difference compared to the previously way parmtop files were generated. Or
I would expect that something should be written out under the flag:
> %FLAG ANGLES_INC_HYDROGEN
> %FORMAT(10I8)
It seems that the changes in the routine above work though with the
'old style' prmtop files even if there are some additional warning issued
by the leap program under NAB like:
1-4: angle 9455 9456 duplicates bond ('triangular' bond) or angle ('square' bond)
Andreas says that the resulting prmtop file then contains more angles
(one for each TIP3P water), that seems to bee all.
So my questions are:
1. What else should I change to make tleap or xleap work and let me write
the angle out
2. Could I change something in the frcmod files so that the angles would
be written out? (I;ve tried to use t/xleap with the MEOH solvent and
indeed I get angles written out there)
3. does leap under NAB write also new style prmtop files?
Any ideas/solutions would be more than welcomed.
Thanks,
Ioana
Received on Tue May 13 2003 - 21:53:01 PDT
