AMBER Archive (2003)

Subject: Re: topology file in large systems

From: caldwell_at_heimdal.compchem.ucsf.edu
Date: Thu Apr 17 2003 - 17:25:49 CDT

Upgrade to Amber7, it is capable of such big systems.

jim

On Thu, 17 Apr 2003, GUILLERMINA L ESTIU wrote:

> 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
> 

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