Re: [AMBER] Problem with tleap (non atom type)

From: David A Case <>
Date: Fri, 18 Aug 2017 16:44:33 -0400

On Fri, Aug 18, 2017, Parviz Seifpanahi Shabane wrote:

> 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.

Bill's response could get you started. But I'm not sure why he didn't just
say the the 5' residues in the standard Amber library to not have phosphate

If you don't need that phosphate (since you are only working with a part
of a bigger molecule, just remove them from your input pdb file.

If you really think you need them, see Section 3.2.3 in the Reference
Manual for instructions.


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Received on Fri Aug 18 2017 - 14:00:02 PDT
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