AMBER Archive (2004)

Subject: AMBER: contributed parameters (modified base - PSU)

From: Shau Grossman (
Date: Tue Feb 17 2004 - 20:14:16 CST

Dear Amber users,

 I am just wondering if the H2 of PSU in the OFF file (
 ) is really the H6 (the hydrogen attached to the C6 in the pyrimidine).
 The second question is how the RESP charges of those modified bases (in
 the OFF file) were generated. The sugar and phosphate charges were
 apparently published in
 J. Comp. Chem., 16,1357-1377(1995). How does one generate the RESP
 charges for the modified bases given the sugar RESP charges
  for the regular bases (G,C,A,T) which was generated using intermolecular
 constraints for sugar equivalencing? I am also wondering if those RESP
 charges of each modified base (appeared in the OFF file) were from the
 RESP charges of the corresponding nucleoside.

 If one would like to generate his or her own RESP charges for
pseudouridine or any modified nucleotide using Amber 7. How would one go
about it? Any suggestion
will be appreciated.
 Thanks for your attention,

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