Re: [AMBER] TER dfinition at the middile of pdb file

From: Jason Swails <>
Date: Fri, 30 Apr 2010 23:29:23 -0400


On Fri, Apr 30, 2010 at 8:41 PM, Homa Azizian <>wrote:

> Hi,
> I have a non-standard residue in my pdb file which define with HETATM.
> after I prepare the parameter for that non-standard residue, and load the
> pdb in xleap, and after saving the pdb file, The "TER" definition come after
> my residue in pdb file. is it mean that it recognize my system as 2 separate
> system and treat it like 2

It means that it will not create a bond between those residues. As a
result, it will make the last amino acid before the TER card the C-terminal
version of that amino acid (and if it's an amino acid that follows the TER
card, it will be the N-terminus the next part) I don't think it means
anything else. Amber prmtop files do not carry chain information like PDB
files do to my knowledge...

chain protein? should I change the HETATOM in original pdb file to ATOM?

This should not be necessary. leap will recognize ATOM and HETATM alike.

> Thank you for replying
> Regards,
> Homa
> _______________________________________________
> AMBER mailing list

Good luck!

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Apr 30 2010 - 21:00:03 PDT
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