Re: [AMBER] Confusion in adding TER cards

From: David A Case <>
Date: Fri, 20 Apr 2012 16:13:28 -0400

On Fri, Apr 20, 2012, Asmita Gupta wrote:
> I have a PDB file containing a single RNA molecule. The chain is defined as
> A. Now the molecule contains 4 MG and 2 Na+ residues, where each MG is in
> coordination with 7 Water molecules. Apart from coordinated waters, the
> file has other extra water molecules also present. When i am trying to load
> this pdb into tleap, i am getting the following error :
> Illegal CONECT record in pdb file
> Illegal CONECT record in pdb file

LEaP should be giving better error messages. The simple thing is just to
ignore the warnings, but better would be to remove the CONECT cards. I'm
guessing that you probably don't want all of the waters that are in the pdb
file as well....think carefully about what your starting model should be.

It's well worth reading Section 5.8.1 of the AmberTools12 Reference Manual on
"Cleaning up protein pdb files for Amber" (also applies to nucleic acids!)


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Received on Fri Apr 20 2012 - 13:30:04 PDT
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