I request the help of someone who has expertise with the Amber force fields.
I would like to perform NAB molecular dynamics for a protein that contains the non-standard amino acid, aminobutyric acid (ABA). Because ABA is a non-standard amino acid, I was unable find a force field that supports it. Hence, I modified the leaprc.ff99SB and all_amino94.lib files to include ABA. However, I have a question regarding the atomic charges that I assigned for ABA. Excerpts from the all_amino94.lib file are below.
ABA is structurally similar to VAL but lacks one of the gamma methyl groups. Consequently, the beta carbon of ABA is bonded to two protons, similar to the beta carbon of LEU. Consequently, I used the 0.045700 charge of LEU HB2 and HB3 for the charges of ABA HB1 and HB2. Then I calculated the ABA CB charge of 0.095500 by decreasing the VAL CB charge of 0.298500 to 0.095500 so that the total charge of the ABA moiety remains neutral. Is this approach viable? If not, can someone please coach me in the proper technique for computing the charges for ABA?
Thanks.
!entry.LEU.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg "N" "N" 0 1 131072 1 7 -0.415700
"H" "H" 0 1 131072 2 1 0.271900
"CA" "CT" 0 1 131072 3 6 -0.051800
"HA" "H1" 0 1 131072 4 1 0.092200
"CB" "CT" 0 1 131072 5 6 -0.110200
"HB2" "HC" 0 1 131072 6 1 0.045700
"HB3" "HC" 0 1 131072 7 1 0.045700
"CG" "CT" 0 1 131072 8 6 0.353100
"HG" "HC" 0 1 131072 9 1 -0.036100
"CD1" "CT" 0 1 131072 10 6 -0.412100
"HD11" "HC" 0 1 131072 11 1 0.100000
"HD12" "HC" 0 1 131072 12 1 0.100000
"HD13" "HC" 0 1 131072 13 1 0.100000
"CD2" "CT" 0 1 131072 14 6 -0.412100
"HD21" "HC" 0 1 131072 15 1 0.100000
"HD22" "HC" 0 1 131072 16 1 0.100000
"HD23" "HC" 0 1 131072 17 1 0.100000
"C" "C" 0 1 131072 18 6 0.597300
"O" "O" 0 1 131072 19 8 -0.567900
!entry.VAL.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
"N" "N" 0 1 131072 1 7 -0.415700
"H" "H" 0 1 131072 2 1 0.271900
"CA" "CT" 0 1 131072 3 6 -0.087500
"HA" "H1" 0 1 131072 4 1 0.096900
"CB" "CT" 0 1 131072 5 6 0.298500
"HB" "HC" 0 1 131072 6 1 -0.029700
"CG1" "CT" 0 1 131072 7 6 -0.319200
"HG11" "HC" 0 1 131072 8 1 0.079100
"HG12" "HC" 0 1 131072 9 1 0.079100
"HG13" "HC" 0 1 131072 10 1 0.079100
"CG2" "CT" 0 1 131072 11 6 -0.319200
"HG21" "HC" 0 1 131072 12 1 0.079100
"HG22" "HC" 0 1 131072 13 1 0.079100
"HG23" "HC" 0 1 131072 14 1 0.079100
"C" "C" 0 1 131072 15 6 0.597300
"O" "O" 0 1 131072 16 8 -0.567900
!entry.ABA.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
"N" "N" 0 1 131072 1 7 -0.415700
"H" "H" 0 1 131072 2 1 0.271900
"CA" "CT" 0 1 131072 3 6 -0.087500
"HA" "H1" 0 1 131072 4 1 0.096900
"CB" "CT" 0 1 131072 5 6 0.095500
"HB1" "HC" 0 1 131072 6 1 0.045700
"HB2" "HC" 0 1 131072 7 1 0.045700
"CG" "CT" 0 1 131072 8 6 -0.319200
"HG1" "HC" 0 1 131072 9 1 0.079100
"HG2" "HC" 0 1 131072 10 1 0.079100
"HG3" "HC" 0 1 131072 11 1 0.079100
"C" "C" 0 1 131072 12 6 0.597300
"O" "O" 0 1 131072 13 8 -0.567900
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Received on Fri Mar 11 2022 - 09:30:02 PST
