This is actually to everyone in the Reflector group,
but to Dr. David Case in particular:
I tried the protonate command on a GATA1:DNA complex
downloaded from the database (1GAT) and got a strange error
message:
(I'll show the output as far as it went also):
Proton substitutions
----------------------------------------
in output file in input file
---------------------------------------- H1 LYS 1 -3.86 11.01 13.32 | 3H
LYS 1 -3.86 11.01 13.32 0.11 H2 LYS 1 -4.64 12.06 14.40 | 2H LYS 1 -4.64
12.06 14.40 0.11 H3 LYS 1 -3.10 11.46 14.77 | 1H LYS 1 -3.10 11.46 14.77
0.11 HB3 LYS 1 -5.89 9.92 16.76 | 1HB LYS 1 -5.89 9.92 16.76 0.01 HB2 LYS
1 -5.19 11.52 16.51 | 2HB LYS 1 -5.19 11.52 16.51 0.01 HG3 LYS 1 -3.73
10.88 18.13 | 1HG LYS 1 -3.73 10.88 18.13 0.01 HG2 LYS 1 -2.94 9.98 16.84
| 2HG LYS 1 -2.94 9.98 16.84 0.01 HD3 LYS 1 -4.17 7.97 17.42 | 1HD LYS 1
-4.17 7.97 17.42 0.01 HD2 LYS 1 -5.16 8.85 18.58 | 2HD LYS 1 -5.16 8.85
18.58 0.01 HE3 LYS 1 -2.16 8.39 18.75 | 1HE LYS 1 -2.16 8.39 18.75 0.01
HE2 LYS 1 -3.38 7.61 19.74 | 2HE LYS 1 -3.38 7.61 19.74 0.01 HZ1 LYS 1
-2.63 10.48 19.72 | 3HZ LYS 1 -2.63 10.48 19.72 0.22 HZ2 LYS 1 -4.06 9.91
20.45 | 2HZ LYS 1 -4.06 9.91 20.45 0.22 HZ3 LYS 1 -2.54 9.39 21.02 | 1HZ
LYS 1 -2.54 9.39 21.02 0.22 HB3 ARG 2 -7.38 7.29 10.76 | 1HB ARG 2 -7.38
7.29 10.76 0.01 HB2 ARG 2 -5.68 7.59 11.11 | 2HB ARG 2 -5.68 7.59 11.11
0.01 HG3 ARG 2 -7.76 9.44 10.03 | 1HG ARG 2 -7.76 9.44 10.03 0.01 HG2 ARG
2 -6.04 9.35 9.66 | 2HG ARG 2 -6.04 9.35 9.66 0.01 HD3 ARG 2 -5.50 10.40
11.81 | 1HD ARG 2 -5.50 10.40 11.81 0.01 HD2 ARG 2 -7.22 10.47 12.22 | 2HD
ARG 2 -7.22 10.47 12.22 0.01 HH11 ARG 2 -6.78 12.08 13.16 | 1HH1 ARG 2
-6.78 12.08 13.16 0.02 HH12 ARG 2 -6.89 13.81 13.13 | 2HH1 ARG 2 -6.89
13.81 13.13 0.01 HH21 ARG 2 -6.76 14.04 9.69 | 1HH2 ARG 2 -6.76 14.04 9.69
0.01 HH22 ARG 2 -6.89 14.91 11.18 | 2HH2 ARG 2 -6.89 14.91 11.18 0.01 HB3
ASP 3 -6.89 5.97 17.19 | 2HB ASP 3 -6.89 5.97 17.19 0.06 HB2 ASP 3 -5.68
5.08 16.28 | 1HB ASP 3 -5.68 5.08 16.28 0.06 HB3 HIS 4 -12.21 6.80 15.84 |
2HB HIS 4 -12.21 6.80 15.84 0.07 HB2 HIS 4 -10.79 6.31 16.68 | 1HB HIS 4
-10.79 6.31 16.68 0.10 HB3 PRO 5 -11.10 8.47 11.34 | 2HB PRO 5 -11.10 8.47
11.34 0.07 HB2 PRO 5 -10.89 7.47 9.88 | 1HB PRO 5 -10.89 7.47 9.88 0.07
HG3 PRO 5 -8.75 7.84 11.48 | 2HG PRO 5 -8.75 7.84 11.48 0.05 HG2 PRO 5
-9.13 6.17 10.95 | 1HG PRO 5 -9.13 6.17 10.95 0.05 HD3 PRO 5 -9.77 7.46
13.63 | 2HD PRO 5 -9.77 7.46 13.63 0.03 HD2 PRO 5 -9.15 5.82 13.31 | 1HD
PRO 5 -9.15 5.82 13.31 0.05 HG21 THR 6 -15.39 1.31 9.15 | 2HG2 THR 6
-15.39 1.31 9.15 0.07 HG22 THR 6 -13.99 0.49 9.89 | 3HG2 THR 6 -13.99 0.49
9.89 0.06 HG23 THR 6 -15.56 0.53 10.72 | 1HG2 THR 6 -15.56 0.53 10.72 0.06
HB3 CYS 7 -13.31 1.97 5.30 | 1HB CYS 7 -13.31 1.97 5.30 0.01 HB2 CYS 7
-12.04 3.20 5.35 | 2HB CYS 7 -12.04 3.20 5.35 0.01 error: error on
computed goto #1 in subr hydros
ip= 13 na= 3 nhyd= 2 protp(1-3,1-4)= -13.31-12.04 0.00 0.00
1.97 3.20 0.00 0.00 5.30
The last 3 lines are the error message--something about the cysteine
made it complain. Any suggestions?
Thanks very much,
Michael Cooney
mike_at_bmb.uga.edu
Received on Wed Aug 30 2000 - 11:40:53 PDT
