Re: [AMBER] Request of help on Leap PDB preparation error "atom does not have a type"

From: David A Case <>
Date: Wed, 30 May 2018 08:46:50 -0400

On Wed, May 30, 2018, 符哲瀚 wrote:
> source leaprc.protein.ff14SB
> source leaprc.water.tip3p
> loadamberparams frcmod.ionsjc_tip3p

Since your PDB file contains DNA, you also have to load a DNA library, e.g.

    source leaprc.DNA.OL15

Also the "leaprc.water.tip3p" also loads the corresponding ion
paramters, so there is no need to load frcmod.ionsjc_tip3p.

> FATAL: Atom .R<DG 1535>.A<C4 22> does not have a type.
> It seems that the certain names of atoms in PDB file cannot be
> recognized by LEAP. I think this is caused by the atoms on DNA chain in
> the structure. (DG, DA, DT, DC are names of basic groups in DNA)

You are correct. Starting in 2016, we split libraries into separate parts for
protein, DNA, RNA, carbohydrates, water/ions, and general organic

....good luck....dac

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Received on Wed May 30 2018 - 06:00:06 PDT
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