Re: [AMBER] system size more than 1000 residues

From: Pengzhi Zhang <>
Date: Wed, 03 Sep 2014 14:23:53 -0500

Now it makes more sense. I generated the prmtop file by inputting a leap
script produced by myself since I am using coarse-grained simulations
and there is no real residue. I probably still made some mistakes
because I did not have 1000 "pseudo residue" types/names. Thank you for
pointing that out. Sincerely, Pengzhi ------------------------------
Message: 7 Date: Tue, 2 Sep 2014 17:39:51 -0400 From: Jason Swails
<> Subject: Re: [AMBER] system size more than 1000
residues To: AMBER Mailing List <> Message-ID:
Content-Type: text/plain; charset=UTF-8 On Tue, Sep 2, 2014 at 5:32 PM,
Pengzhi Zhang <> wrote:

> 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 BioMaPS, Rutgers University Postdoctoral Researcher

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Received on Wed Sep 03 2014 - 12:30:02 PDT
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