AMBER Archive (2009)

Subject: [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off - different labels

From: Tomasio, Susana (S.M.T.Tomasio_at_warwick.ac.uk)
Date: Wed May 27 2009 - 06:25:35 CDT

Hi all

I noticed that the N-cap residue Acetyl (ACE) in the amoeba force field is in two files (amoeba_amino.off and amoeba_aminont.off),
but has different atom labels (2nd column): One is labelled with numbers and the other one is labelled with letters.
In the amoeba_amino.off:
"HH31" "181" 0 1 131072 1 1 0.076010
 "CH3" "180" 0 1 131072 2 6 -0.190264
 "HH32" "181" 0 1 131072 3 1 0.076011
 "HH33" "181" 0 1 131072 4 1 0.076010
 "C" "182" 0 1 131072 5 6 0.512403
 "O" "183" 0 1 131072 6 8 -0.550170

And in the amoeba_aminont.off:
"HH31" "HC" 0 1 131072 1 1 0.112300
 "CH3" "CT" 0 1 131072 2 6 -0.366200
 "HH32" "HC" 0 1 131072 3 1 0.112300
 "HH33" "HC" 0 1 131072 4 1 0.112300
 "C" "C" 0 1 131072 5 6 0.597200
 "O" "O" 0 1 131072 6 8 -0.567900

When I tried to load the ACE residue it didn't work, but by changing the 2nd column in the amoeba_aminont.off to include the labels that are in the the amoeba_amino.off file, it did work.

I was wondering if what I did is ok.

Thank you,

Susana
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