Re: [AMBER] Regarding generating parameters for protein with NAD+

From: case <>
Date: Wed, 11 Dec 2013 21:19:34 -0500

On Wed, Dec 11, 2013, Prema Mallipeddi wrote:

> 4) loadoff NAD+.lib
> 5) complex = loadpdb 2gdz_nad.pdb
> Created a new atom named: PA within residue: .R<NDP 266>

This means that there is an atom named "PA" in the pdb file, but there is no
atom named "PA" in the library file (presumably in NAD+.lib). You must make
sure that the atom and residue names in the PDB match those in the libary.

> Added missing heavy atom: .R<NDP 266>.A<P1 1>

Similarly, this means that there is an atom named "P1" in the library file,
but not matching atom is found in the pdb file. So it sounds like the names
in the libary file you are using are (almost) completely different than the
atom names in your pdb file. You have to change one or the other to make them


AMBER mailing list
Received on Wed Dec 11 2013 - 18:30:03 PST
Custom Search