AMBER Archive (2002)

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

From: Ling Zhang (lz267_at_nyu.edu)
Date: Thu Jun 13 2002 - 16:41:08 CDT

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