When doing multiple conformer charge fitting, in the resp input files
there is a section with the atom equivalences between the conformers.
Something like this (for five conformations):
5
1 1 2 1 3 1 4 1 5 1
5
1 2 2 2 3 2 4 2 5 2
5
1 3 2 3 3 3 4 3 5 3
5
1 4 2 4 3 4 4 4 5 4
5
1 5 2 5 3 5 4 5 5 5
5
1 6 2 6 3 6 4 6 5 6
...
Reading some sources it says that all atoms in the molecule should be
present in this section, while other seem suggesting that there should
be only those atoms which are note affected by conformational change.
However, in the example provided with amber6 (bis-napthyl), this section
is complete in the bis_1.in, but not in the bis_2.in (only two atoms).
2
1 18 2 18
2
1 28 2 28
Could somebody explain me how works this section? What shoud I do for
making a multiple conformer charge fittting?
Finally another question: I have read that this last section equates
the charges for the same atom in the different conformers, so it seems
that in the *2.out the charges for the same atom should be she same.
However, I have seen the charges are different (even when the last
section is complete in the *1.in and *2.in input files for resp). Could
somebody explain me this?
Thank you very much,
Miguel.
Received on Thu Jun 20 2002 - 16:05:11 PDT
