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AMBER Archive (2007)Subject: AMBER: "Atom valence violated" from LEaP
From: Francesco Pietra (chiendarret_at_yahoo.com)
I am using DOCK6.1 and Amber9 with a pore protein model.
>From the model deprived of the single (natural) residue HOH from the pore, I
Now I wanted to repeat all the above sequence with the natural residue HOH in
ATOM 3412 O THR X 444 -15.798 15.199 24.830 0.00 0.00 O
TER 3413 THR X 444
HETATM 3414 O HOH X 448 -0.036 0.094 -2.262 0.00 0.00 O
END
Now, LEaP did the job, though grid generation in Chimera complained (on loading
WARNING: assign_vdw_labels: Atom valence violated for xxxx.inpcrd
Chimera was right. The internal water residue was now triangulated. The H-H
The last portion of the coordinate section of the mol2 reads:
6884 OXT -13.9375 14.3278 24.9443 O.co2 444 THR444 -0.8044
6885 O -0.0360 0.0940 -2.2620 O.t3p 445 WAT445 -0.8340
6886 H1 0.9212 0.0940 -2.2620 H.t3p 445 WAT445 0.4170
6887 H2 -0.2760 1.0206 -2.2620 H.t3p 445 WAT445 0.4170
and that mol2 ends with:
443 GLU443 6857 RESIDUE 4 A GLU 2
444 THR444 6872 RESIDUE 4 A THR 1
445 WAT445 6886 RESIDUE 4 A WAT 0 ROOT
Must add that the model before removing all hydrogen atoms showed the HOH
Perhaps the protocol to follow is different from the one I followed. Removing
Thanks
francesco pietra
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