AMBER Archive (2002)

Subject: Re: The atom number mismatch in coord and topology file.

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Thu Jun 13 2002 - 17:27:38 CDT

Which AMBER version? We can't help
without that. Things are different in
AMBER 7, especially for large systems.

----- Original Message -----
From: "Ling Zhang" <lz267_at_nyu.edu>
To: "amber reflector" <amber_at_heimdal.compchem.ucsf.edu>
Sent: Thursday, June 13, 2002 5:41 PM
Subject: The atom number mismatch in coord and topology file.

> Dear all,
>
> When I carried out minimization while holding a part of the system
restrained, the mdout file showed that the atom number is mismatched in
constraint coord and topology files. But the toltal atom number displayed in
the coord and topolygy files were the same 103250. The coord file and
topolygy file were generated from Leap which worked well when I generated
the coord and topology files for the other small system.
> Is it possible that Leap will give wrong coord and topolygy files when
the system is big, such as 103250 atoms in my case? Then how to fix it?
> Thanks a lot.
>
> Ling
>
>