AMBER Archive (2006)

Subject: Re: AMBER: Qestion about input for RESP program

From: FyD (fyd_at_u-picardie.fr)
Date: Thu May 25 2006 - 10:53:28 CDT

Quoting JunJun Liu <ljjlp03_at_gmail.com>:

> Thanks to Ilyas and Francois! I have a further question on this issue. I
> got the following charge constraints with R.E.D.II for a multi-orientation
> calculation. According to my understanding, it means the sum of atom 1
> from all molecule orientation is constrained to be zero. And so does to
> atom 2 in all molecules, atom 3 in all molecules.... But this is nonsense
> to me. Or does the charge constraint input have another definiation method
> for multi-molecules? Thanks!

Here I think you mix up intra or inter-molecular charge restraint with multiple
structure (structure= molecule or conformation or orientation) charge
restraint.

Please look at the RESP inputs in a R.E.DD.B. project, for instance the F-60:

Intra and/or inter-molecular charge restraints for atom or group of atoms
    6 0.000000
    1 10 1 11 1 12 1 13 5 1 5 2
    6 0.000000
    1 1 1 2 1 3 1 4 5 3 5 4

Inter-'molecular' charge equivalencing (i.e. for different orientations or
conformations)
    4
    1 1 2 1 3 1 4 1
    4
    1 2 2 2 3 2 4 2
    4
    1 3 2 3 3 3 4 3
...
Inter-'molecular' charge equivalencing (i.e. for different molecules)
    8
    5 1 17 1 29 1 41 1 53 1 59 1 65 1 71 1
    8
    5 2 17 2 29 2 41 2 53 2 59 2 65 2 71 2

Also look at the RESP manual...

regards, F.

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