[Dock-fans] Long bonds
Francesco Pietra
chiendarret at yahoo.com
Mon Oct 22 13:37:01 PDT 2007
With my large protein and ligand I was able to carry out docking, both rigid
and flex ligand. Amber_score failed because of two kinds of problems with the
protein.
1st PROBLEM (protons on histidine, etc):
FATAL: Atom .R<GLU 443>.A<HE1 16> does not have a type.
FATAL: Atom .R<HIE 441>.A<HD1 18> does not have a type.
FATAL: Atom .R<ASP 402>.A<HD1 13> does not have a type.
FATAL: Atom .R<ASP 386>.A<HD1 13> does not have a type.
FATAL: Atom .R<HIE 380>.A<HD1 18> does not have a type.
FATAL: Atom .R<ASP 375>.A<HD1 13> does not have a type.
FATAL: Atom .R<GLU 373>.A<HE1 16> does not have a type.
FATAL: Atom .R<GLU 332>.A<HE1 16> does not have a type.
FATAL: Atom .R<HIE 330>.A<HD1 18> does not have a type.
FATAL: Atom .R<ASP 291>.A<HD1 13> does not have a type.
FATAL: Atom .R<ASP 275>.A<HD1 13> does not have a type.
FATAL: Atom .R<HIE 269>.A<HD1 18> does not have a type.
FATAL: Atom .R<ASP 264>.A<HD1 13> does not have a type.
FATAL: Atom .R<GLU 262>.A<HE1 16> does not have a type.
FATAL: Atom .R<GLU 221>.A<HE1 16> does not have a type.
FATAL: Atom .R<HIE 219>.A<HD1 18> does not have a type.
FATAL: Atom .R<ASP 180>.A<HD1 13> does not have a type.
FATAL: Atom .R<ASP 164>.A<HD1 13> does not have a type.
FATAL: Atom .R<HIE 158>.A<HD1 18> does not have a type.
FATAL: Atom .R<ASP 153>.A<HD1 13> does not have a type.
FATAL: Atom .R<GLU 151>.A<HE1 16> does not have a type.
FATAL: Atom .R<GLU 128>.A<HE1 16> does not have a type.
FATAL: Atom .R<GLU 110>.A<HE1 16> does not have a type.
FATAL: Atom .R<HIE 108>.A<HD1 18> does not have a type.
FATAL: Atom .R<ASP 69>.A<HD1 13> does not have a type.
FATAL: Atom .R<ASP 53>.A<HD1 13> does not have a type.
FATAL: Atom .R<HIE 47>.A<HD1 18> does not have a type.
FATAL: Atom .R<ASP 42>.A<HD1 13> does not have a type.
FATAL: Atom .R<GLU 40>.A<HE1 16> does not have a type.
FATAL: Atom .R<GLU 17>.A<HE1 16> does not have a type.
FATAL: Atom .R<NSER 1>.A<H 14> does not have a type.
Is that better in such cases to edit the names by hand (problematic with
aspartic, H on O), or make recourse to (a) downlodable sourceforge softw, (b)
"biophysics" softw on server?
----------------------------
2nd PROBLEM:
WARNING: There is a bond of 50.040630 angstroms between:
------- .R<THR 333>.A<C 13> and .R<SER 334>.A<N 1>
WARNING: There is a bond of 39.464740 angstroms between:
------- .R<THR 222>.A<C 13> and .R<SER 223>.A<N 1>
WARNING: There is a bond of 49.372740 angstroms between:
I was advised to insert "TER" records between the residues that the bond is
connecting. For the first long bond, is that correct as follows:
ATOM 5140 N THR X 333 13.448 -15.558 22.741 0.00 0.00
ATOM 5141 H THR X 333 12.608 -15.012 22.643 0.00 0.00
ATOM 5142 CA THR X 333 14.691 -14.863 22.954 0.00 0.00
ATOM 5143 HA THR X 333 15.655 -15.355 22.580 0.00 0.00
ATOM 5144 CB THR X 333 14.648 -13.582 22.114 0.00 0.00
ATOM 5145 HB THR X 333 15.582 -13.069 22.291 0.00 0.00
ATOM 5146 CG2 THR X 333 14.455 -13.769 20.605 0.00 0.00
ATOM 5147 HG21 THR X 333 14.158 -12.806 20.145 0.00 0.00
ATOM 5148 HG22 THR X 333 15.321 -14.161 20.049 0.00 0.00
ATOM 5149 HG23 THR X 333 13.626 -14.520 20.409 0.00 0.00
ATOM 5150 OG1 THR X 333 13.670 -12.723 22.556 0.00 0.00
ATOM 5151 HG1 THR X 333 12.831 -13.194 22.522 0.00 0.00
ATOM 5152 C THR X 333 14.755 -14.634 24.443 0.00 0.00
ATOM 5153 O THR X 333 15.694 -15.150 25.132 0.00 0.00
TER
ATOM 5154 N SER X 334 -16.176 22.312 10.940 0.00 0.00
ATOM 5155 H SER X 334 -15.301 22.760 10.966 0.00 0.00
ATOM 5156 CA SER X 334 -16.224 20.932 11.429 0.00 0.00
ATOM 5157 HA SER X 334 -17.198 20.770 11.905 0.00 0.00
ATOM 5158 CB SER X 334 -15.868 19.959 10.306 0.00 0.00
ATOM 5159 HB2 SER X 334 -15.761 18.918 10.709 0.00 0.00
ATOM 5160 HB3 SER X 334 -14.903 20.280 9.956 0.00 0.00
ATOM 5161 OG SER X 334 -16.906 19.973 9.300 0.00 0.00
ATOM 5162 HG SER X 334 -16.948 20.844 8.983 0.00 0.00
ATOM 5163 C SER X 334 -15.185 20.856 12.533 0.00 0.00
ATOM 5164 O SER X 334 -14.212 21.643 12.566 0.00 0.00
Thanks
francesco pietra
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