protonate

Protonate entry

This information is obsolete. In Amber <5, all this is done automatically by leap, based on the data in the prep.in file.

Necessary only if you want to protonate the molecule from a crystal structure
File: $OML_AMBER/dat/Mumod/PROTON_INFO.Ulf

One entry for each molecule
First row: residue name, #non-hydrogen atoms
Second row: a list of the non-hydrogen atom names (upto 20 on each row)
Third row: the number of types of hydrogen atoms (i.e. the number of heavy atoms which bind hydrogen atoms = the number of rows following this line)
Following rows (one for each hydrogens): protonation type, involved atom numbers, name of the hydrogen atom

The appropriate types are best found from similar atoms in the amino acids.

Examples of various types:

1: One H on a sp2 C atom in a ring. Give the C atom followed by its two neighbours (in any order).

1 1 2 3 H ; for H-C1<

C3

2: A methine group: two Hs on a sp3 C atom. Give the C atom followed by its two neighbours (in any order).

H1

2 1 2 3 H1 H2 ; for C2-C1-C3

H2

2: One Hs on a sp3 C atom. Give the C atom followed by its three neighbours (in any order).

H

3 1 2 3 4 H ; for C2-C1-C3

C4

5: A methyl group: three Hs on a sp3 C atom. Give the C atom followed by its neighbour and the neighbour's neighbour (in this order).

5 1 2 3 H1 H2 H3 ; for H1/2/3-C1-C2-C3

7: One H on a sp3 O. Give the O atom followed by its neighbour and the neighbour's neighbour (in this order):

7 1 2 3 H ; for H-O1-C2-C3

Sample entry (chatecol = phenol with an extra ortho O- group = O2)

CAT 8
C1 C2 C3 C4 C5 C6 O1 O2
5
1 3 2 4    H3
1 4 3 5    H4
1 5 4 6    H5
1 6 5 1    H6
7 7 1 2    H1