Re: [AMBER] atom type issue in tleap with ff-nucleic-OL15

From: David A Case <>
Date: Wed, 8 Sep 2021 08:02:23 -0400

On Tue, Sep 07, 2021, Aliakbartehrani Zahra wrote:
>I would like to prepare .parm and .top files for my B-DNA model (1bna PDB
>code) using ff-nucleic-OL15 (OL Force Field Refinement for RNA and DNA
>Simulations (<>) with AMBER 16. I have
>used the following input for tleap and have modified the pdb input file
>for both atom types (O’3H and O’5H) and residue names (DC5 and DG3 in each
>strand) at 3’ and 5’ terminals.

>FATAL: Atom .R<DC 1>.A<HO5' 31> does not have a type.

You should not need to modify the input pdb file, as tleap will add
hydrogens for you, and fix up the ends. Plus, it looks like you are giving
incorrect hydrogen atom names: as the message above indicates, the hydrogen
on the 5' end is called HO5', not O'5H. (But all this is odd, since 1bna
doesn't have any hydrogens, so it's not clear how you modified the input pdb

I think if you look at the full output from tleap, it will point out
problems like this as the PDB file is processed.

Note also that you can load ff-nucleic-OL15 directly in tleap by using
"source leaprc.DNA.OL15". It may be that the ff-nucleic-OL15.lib file you
are using has some problems, so I would recommend using the ones bundled
with Amber.


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Received on Wed Sep 08 2021 - 05:30:02 PDT
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