Re: [AMBER] system size more than 1000 residues

From: Jason Swails <>
Date: Tue, 2 Sep 2014 17:39:51 -0400

On Tue, Sep 2, 2014 at 5:32 PM, Pengzhi Zhang <>

> Thanks Jason for the reply. Sorry that I missed the email from the mailing
> list.
> It recycles after 999 because in the prmtop file, the residue labels are
> written in the format of a4, and I assume the last character of the four
> should be space as separation.

​I think you're conflating residue number and residue name. The prmtop
file doesn't store residue numbers (it stores the first atom of each
residue...), so Amber simply treats residue numbers as sequential (i.e.,
residues are numbered from 1 to the number of residues regardless of what
is in the starting PDB). The residue label simply tells you what name that
residue is. For example, ALA for alanine, GLY for glycine, etc. And as
you'd imagine, many of them repeat.

​Also, there is no requirement for space delimiting strings in the prmtop
file. It's common for atom names to be 4 characters, so in many cases
there are no spaces between atom names of adjacent atoms.​ And the residue
names should be set by the library files -- how are you possibly getting a
unique (and numbered!) residue name for each residue??

How are you making this prmtop file?

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Sep 02 2014 - 15:00:02 PDT
Custom Search