In leap, 'desc DA5' to see the correct atom names for the phosphate
groups, and edit your pdb to match.
Bill
On 8/18/17 7:51 AM, Parviz Seifpanahi Shabane wrote:
> Dear AMBER user,
> I used Pymol to cut-off part of the PDB file (1Kx5 Structure of the
> Nucleosome Core Particle) it is very big molecules and I just want to work
> with the part of it (slice of it that has histone tail H4) for making my
> box smaller and run the faster simulations. I used this new PDB file for
> creating BOX (OPC+FF10 SB) and I am getting the "does not have a type"
> error:
> FATAL: Atom .R<DA5 -32>.A<P 31> does not have a type.
> FATAL: Atom .R<DA5 -32>.A<OP1 32> does not have a type.
> FATAL: Atom .R<DA5 -32>.A<OP2 33> does not have a type.
> FATAL: Atom .R<DT5 47>.A<P 31> does not have a type.
> FATAL: Atom .R<DT5 47>.A<OP1 32> does not have a type.
> FATAL: Atom .R<DT5 47>.A<OP2 33> does not have a type.
> FATAL: Atom .R<DT5 53>.A<P 31> does not have a type.
> FATAL: Atom .R<DT5 53>.A<OP1 32> does not have a type.
> FATAL: Atom .R<DT5 53>.A<OP2 33> does not have a type.
> FATAL: Atom .R<DG5 61>.A<P 32> does not have a type.
> FATAL: Atom .R<DG5 61>.A<OP1 33> does not have a type.
> FATAL: Atom .R<DG5 61>.A<OP2 34> does not have a type.
> I tried to
> any suggestion?
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Received on Fri Aug 18 2017 - 10:30:03 PDT
