Dear Amber user's
I am generating the solvent file using command
ambpdb -aatm -p protein.top <protein_min.crd> protein_solvent.pdb
When the protein is lengthy, its causing format problem during tleap run.
The real homodimer with a and b chain have the same number of chain and the
same numbering
ATOM 5789 CZ ARG A 728 30.165 64.691 85.588 1.00
82.20 C
ATOM 5790 NH1 ARG A 728 31.373 64.164 85.772 1.00
81.01 N
ATOM 5791 NH2 ARG A 728 29.094 64.075 86.079 1.00
80.81 N
TER 5792 ARG A
728
ATOM 5793 N THR B 6 34.101 83.914 30.674 1.00
79.98 N
ATOM 5794 CA THR B 6 32.622 83.701 30.563 1.00
80.68 C
ATOM 5795 C THR B 6 32.271 82.198 30.415 1.00
80.99 C
ATOM 5796 O THR B 6 31.458 81.827 29.552 1.00
82.28 O
If you see below the chain is ending at 2163 and the chain b is starting
from 2164 instead of 1.
ATOM 34303 C ARG 2163 5.387 47.227 -15.222 1.00
0.00
ATOM 34304 O ARG 2163 5.611 47.786 -14.144 1.00
0.00
ATOM 34305 OXT ARG 2163 5.440 47.901 -16.248 1.00
0.00
TER
ATOM 34306 N THR 2164 -15.132 51.856 34.718 1.00
0.00
ATOM 34307 H1 THR 2164 -14.494 51.092 34.890 1.00
0.00
ATOM 34308 H2 THR 2164 -15.462 51.795 33.765 1.00
0.00
This cause error on running tlesp.If I reduce gap between ATOM and the
number 34303, tleap is reading full residue ARG otherwise it reads RG and
causing fatal error.
Does someone has solution to this problem or script to correct the pdb
format?
Regards
*Krati Sharma*
*
*
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Received on Thu Sep 05 2013 - 20:30:03 PDT
