AMBER Archive (2001)

Subject: Mystery protons!

From: Sanjeev B.S. (sanjeev_at_mbu.iisc.ernet.in)
Date: Sun Aug 26 2001 - 07:03:11 CDT

Hello,
        I picked up a ligand from an old AMBER(4.1) generated PDB and ran
'protonate' on it. It gave the following error message. I am surprised to
see this as these atoms are present in all_nuc94.in, for instance. I have
set the AMBERHOME variable right. I don't know whatelse I should do to get
over this problem. Help please!

Thanks very much,

Sincerely,
-Sanjeev

---------------------------Error Mesage----------------------------------------
Here are the mystery protons from input file:

H5T RU5 134 -3.79 2.13 3.83
H5'1 RU5 134 -5.86 2.87 1.99
H5'2 RU5 134 -5.08 1.28 2.05
H4' RU5 134 -3.63 3.93 1.56
H1' RU5 134 -1.15 3.27 0.71
H6 RU5 134 -1.87 -0.19 1.40
H5 RU5 134 -0.34 -2.02 0.84
H3 RU5 134 1.76 0.53 -1.70
H3' RU5 134 -4.47 1.68 -0.31
H2'1 RU5 134 -2.55 1.94 -1.51
HO'2 RU5 134 -3.05 4.57 -1.14