AMBER Archive (2003)

Subject: topology file in large systems

From: GUILLERMINA L ESTIU (gle10_at_psu.edu)
Date: Thu Apr 17 2003 - 16:58:35 CDT

I am having trouble with the topology file for a system that has 36300 atoms
(before solvating with a water box)
I am using amber6.
In the dihedral arrays, the "atom number" (~36300x3) goes to 108900. When the
third or fourth atoms that define the dihedral are negative, they do not fit
the reading format (12I6) (rdparam.f)
I do not know which subroutine generates the topology file. I think that I need
to set the writing format of KP, LP, KPH and LPH to I7

The following are two lines of the dihedral array of the top files. A negative
value appears in the second line
100938100944100950100953 9100938100944100950100956 9101046101043
101049101052 1101046101043-101049101052 2101043101049101055101058

Thanks for your help
Dr Guillermina Estiu
Chemistry Department
Pennsylvania State University
PA 16802