Hi, I got an error on tleap.
Loading PDB file: ./1gh0.pdb
(starting new molecule for chain B)
(starting new molecule for chain C)
(starting new molecule for chain D)
(starting new molecule for chain E)
(starting new molecule for chain F)
(starting new molecule for chain A)
(starting new molecule for chain B)
(starting new molecule for chain C)
(starting new molecule for chain D)
(starting new molecule for chain E)
(starting new molecule for chain F)
Added missing heavy atom: .R<MEN 234>.A<OXT 3>
ERROR: Comparing atoms
.R<MEN 234>.A<ND2 15>,
.R<MEN 234>.A<HE21 18>,
.R<MEN 234>.A<HE22 19>, and
.R<MEN 234>.A<HE23 20>
to atoms
.R<MEN 234>.A<ND2 15>,
.R<ALA 1>.A<N 1>,
.R<MEN 234>.A<HE21 18>, and
.R<MEN 234>.A<HE22 19>
This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 142
!FATAL: Message: Atom named N from ALA did not match !
!
!ABORTING.
There is two modified residue on the PDB (1GH0 chain A-F), CYC and MEN. I
just followed the instruction on tutorial B5 simulating the Green
Fluorescent Protein (
http://ambermd.org/tutorials/basic/tutorial5/). MEN
has a type of linking, according to the mailing list (
http://archive.ambermd.org/201608/0419.html), I have to edit MEN.cif and
remove the "linking" word on the "_chem_comp.type".
So, what is the solution for this error ? Thanks.
nb : I used amber 16 and centOS 7 with no GUI
*С уважением*
*Elka Firmanda*
Graduate Student
Department of Physics
Faculty of Mathematics and Natural Sciences
Bogor Agricultural University, Indonesia 16680
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Received on Sun Oct 02 2016 - 23:00:02 PDT
