Re: [AMBER] Problem in creating prmtop inpcrd file in leap

From: David A Case <>
Date: Tue, 24 Jun 2014 21:20:52 -0400

On Tue, Jun 24, 2014, 肖立 wrote:

> Created a new atom named: 'H5' within residue: .R<RA 39>
> Created a new atom named: 'HO2 within residue: .R<RA 39>

Wow. Lots of things to suggest, even though you gave practically no
information about which version of Amber you have, which leaprc file you used,
where you got the PDB file from, etc.

1. It looks you are using an old PDB file: there are no longer residues
named "RA" in Amber (they are just "A", etc., like in the PDB). It's
recommended to update to the current version of AmberTools.

2. It looks(?) like the atom names for H5'' and HO2' in adenine residues
are mangled. A simple thing is to just remove these, and let LEaP build
them back in. Or, fix them in the PDB file: the atom names need to be in
columns 13-16 of an ATOM card (with the "H" in column 13 if there are four
characters in the name).

...good luck....dac

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Received on Tue Jun 24 2014 - 18:30:03 PDT
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