AMBER Archive (2003)

Subject: AMBER pdb help - lost atoms - Part 2

From: kxg2248_at_njit.edu
Date: Thu Apr 03 2003 - 09:39:23 CST

Thanks for the responses on my first post. I've tried even more methods to
get my pdb file to be completely read in, but even starting with nukit,
then nucgen, then leap or antechamber doesn't seem to work. And leap
insists on adding the sugar and phosphate to each base, and I am not using
them in my study.

So here's my pdb file, maybe someone will see something obvious that I've
been missing. I even took out the ligand, thinking that three fragments
may be too much, but that didn't help either. I used the DCN3 and DGN3
designations as per the Amber7 manual (p. 40) to get neutral bases capped
by hydrogens.

Could there be an inherent problem in using only one base pair?

Thanks,
K. Gilbert
NJIT

PDB file:
COMPND GC
ATOM 1 C1 DCN3 1 2.1472 -4.424 2.4696
ATOM 2 N1 DCN3 1 -2.157 -2.191 -0.174
ATOM 3 H1 DCN3 1 -2.098 -1.226 -0.465
ATOM 4 H2 DCN3 1 -2.992 -2.728 -0.366
ATOM 5 C4 DCN3 1 -1.142 -2.754 0.4626
ATOM 6 N3 DCN3 1 -0.054 -2.012 0.7042
ATOM 7 C2 DCN3 1 1.0164 -2.539 1.3482
ATOM 8 O2 DCN3 1 2.0354 -1.878 1.5860
ATOM 9 N2 DCN3 1 0.9622 -3.867 1.7629
ATOM 10 C6 DCN3 1 -0.137 -4.626 1.5243
ATOM 11 C5 DCN3 1 -1.224 -4.118 0.8821
TER
ATOM 12 C7 DGN3 2 0.9446 5.5853 -1.569
ATOM 13 N4 DGN3 2 2.2610 0.9093 0.4863
ATOM 14 H3 DGN3 2 2.1932 -0.040 0.7906
ATOM 15 H4 DGN3 2 3.1036 1.4041 0.6068
ATOM 16 O6 DGN3 2 -2.085 0.4135 -0.876
ATOM 17 C8 DGN3 2 -1.130 1.1864 -0.800
ATOM 18 C9 DGN3 2 -1.035 2.5301 -1.228
ATOM 19 N5 DGN3 2 -1.983 3.3480 -1.848
ATOM 20 C10 DGN3 2 -1.359 4.4859 -2.012
ATOM 21 N6 DGN3 2 -0.059 4.4880 -1.551
ATOM 22 C11 DGN3 2 0.1464 3.2247 -1.043
ATOM 23 N7 DGN3 2 1.3009 2.7773 -0.482
ATOM 24 C12 DGN3 2 1.2138 1.5101 -0.087
ATOM 25 N8 DGN3 2 0.0731 0.7456 -0.222
ATOM 26 H5 DGN3 2 0.0628 -0.199 0.1041
TER
CONECT 1 9
CONECT 2 3 4 5
CONECT 3 2
CONECT 4 2
CONECT 5 2 6 11
CONECT 6 5 7
CONECT 7 6 9 8
CONECT 8 7
CONECT 9 7 10 1
CONECT 10 9 11
CONECT 11 10 5
CONECT 12 21
CONECT 13 24 15 14
CONECT 14 13
CONECT 15 13
CONECT 16 17
CONECT 17 18 25 16
CONECT 18 22 17 19
CONECT 19 20 18
CONECT 20 21 19
CONECT 21 22 20 12
CONECT 22 18 23 21
CONECT 23 24 22
CONECT 24 25 23 13
CONECT 25 17 24 26
CONECT 26 25
END