AMBER Archive (2006)

Subject: AMBER: SAVEPDB in Xleap could not save 4 character atom names

From: Jiayun Pang (PangJ1_at_Cardiff.ac.uk)
Date: Mon May 29 2006 - 11:38:22 CDT

Dear Amber users,
I tried to use xleap (amber8) to read in the structure of NADH, add hydrogens
and save it as a PDB file for some simulation. Xleap read in the structure
without any problem but when I used "savepdb" to save the structure, it gave the
following message

Non-[HED] atom name (NC1') too long for PDB standard - TRIMMING LAST CHARACTER
Non-[HED] atom name (NH1') too long for PDB standard - TRIMMING LAST CHARACTER
Non-[HED] atom name (NC2') too long for PDB standard - TRIMMING LAST CHARACTER
Non-[HED] atom name (NH2') too long for PDB standard - TRIMMING LAST CHARACTER
Non-[HED] atom name (NO2') too long for PDB standard - TRIMMING LAST CHARACTER
Non-[HED] atom name (NHO2) too long for PDB standard - TRIMMING LAST CHARACTER
.............................
..........................

which trimed some of the 4 letter atom names. My initial NADH pdb is as the
following

ATOM 5562 NO7 NAD 600 15.439 51.537 20.402 1.00 20.17
ATOM 5563 NC7 NAD 600 14.253 52.135 20.300 1.00 22.02
ATOM 5564 NN7 NAD 600 14.251 53.481 20.298 1.00 23.63
ATOM 5567 NC3 NAD 600 12.982 51.358 20.254 1.00 22.66
ATOM 5568 NC4 NAD 600 11.711 51.983 20.148 1.00 24.01
ATOM 5570 NC5 NAD 600 10.584 51.131 20.025 1.00 24.48
ATOM 5572 NC6 NAD 600 10.658 49.778 20.173 1.00 24.08
ATOM 5574 NC2 NAD 600 13.037 49.962 20.308 1.00 22.73
ATOM 5576 NN1 NAD 600 11.897 49.233 20.260 1.00 23.82
ATOM 5577 NC1' NAD 600 12.002 47.794 20.133 1.00 23.51
ATOM 5579 NC2' NAD 600 11.045 46.903 20.882 1.00 24.23
ATOM 5581 NO2' NAD 600 11.638 46.538 22.126 1.00 24.05
ATOM 5583 NC3' NAD 600 10.754 45.781 19.866 1.00 23.14
ATOM 5586 NO4' NAD 600 11.690 47.609 18.722 1.00 24.57
ATOM 5587 NC4' NAD 600 10.877 46.474 18.495 1.00 23.73
ATOM 5589 NC5' NAD 600 9.514 46.772 17.900 1.00 22.66
..........................
.........................

where I have made sure that the atom names occupy column 13-16 and these atom
names are directly taken from the PDB file in protein data bank. The pdb file
saved by xleap is like the following

ATOM 1 NC6 NAD 1 10.658 49.778 20.173 1.00 0.00
ATOM 2 NH6 NAD 1 9.744 49.194 20.221 1.00 0.00
ATOM 3 NC5 NAD 1 10.584 51.131 20.025 1.00 0.00
ATOM 4 NH5 NAD 1 9.604 51.531 19.811 1.00 0.00
ATOM 5 NC4 NAD 1 11.711 51.983 20.148 1.00 0.00
ATOM 6 1H4 NAD 1 11.769 52.641 19.277 1.00 0.00
ATOM 7 2H4 NAD 1 11.572 52.599 21.040 1.00 0.00
ATOM 8 NC3 NAD 1 12.982 51.358 20.254 1.00 0.00
ATOM 9 NC7 NAD 1 14.253 52.135 20.300 1.00 0.00
ATOM 10 NO7 NAD 1 15.439 51.537 20.402 1.00 0.00
ATOM 11 NN7 NAD 1 14.251 53.481 20.298 1.00 0.00
ATOM 12 1H7 NAD 1 15.113 53.995 20.331 1.00 0.00
ATOM 13 2H7 NAD 1 13.381 53.991 20.285 1.00 0.00
ATOM 14 NC2 NAD 1 13.037 49.962 20.308 1.00 0.00
ATOM 15 NH2 NAD 1 14.005 49.476 20.351 1.00 0.00
ATOM 16 NN1 NAD 1 11.897 49.233 20.260 1.00 0.00
ATOM 17 NC1 NAD 1 12.002 47.794 20.133 1.00 0.00
ATOM 18 NH1 NAD 1 12.999 47.367 20.277 1.00 0.00
ATOM 19 NC2 NAD 1 11.045 46.903 20.882 1.00 0.00
ATOM 20 NH2 NAD 1 10.038 47.297 21.004 1.00 0.00
ATOM 21 NO2 NAD 1 11.638 46.538 22.126 1.00 0.00
ATOM 22 NHO NAD 1 11.389 47.213 22.760 1.00 0.00
ATOM 23 NC3 NAD 1 10.754 45.781 19.866 1.00 0.00
ATOM 24 NH3 NAD 1 9.844 45.189 19.971 1.00 0.00
ATOM 25 NO3 NAD 1 11.828 44.862 20.035 1.00 0.00
ATOM 26 NHO NAD 1 11.975 44.813 20.982 1.00 0.00
ATOM 27 NC4 NAD 1 10.877 46.474 18.495 1.00 0.00
ATOM 28 NH4 NAD 1 11.354 45.816 17.768 1.00 0.00
ATOM 29 NO4 NAD 1 11.690 47.609 18.722 1.00 0.00
ATOM 30 NC5 NAD 1 9.514 46.772 17.900 1.00 0.00
................................
..............................

As NADH is often used, I wonder if anyone had this problem before. How could I
save the atoms with its original 4 character names in xleap without renaming
them? Many thanks for your advice.

All the best,

Jiayun
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