Re: AMBER: problem with protein minimization

From: David A. Case <>
Date: Mon, 21 Feb 2005 16:11:37 -0800

On Mon, Feb 21, 2005, yen li wrote:

> but with the straight chain, it gives error
> for some of the parameters of sizes.h header file. The
> output file is given below. I also tried changing the
> indicated parameters and then recompiling, but it
> didnt help.

Did the numbers in the error message change when you increased MAX_ISTACK?
(They should, especially that lastist value). Sometimes you have to keep
increasing this value until the program is happy.

> Exceeding lastist in get_istack
> lastist = 30000000
> top_stk= 21868392
> isize = 21027300
> request= 42895692
> Increase MAX_ISTACK in sizes.h and recompile

Sander is not written efficiently for doing a simulation of a very long
straight chain. Mike Crowley might give you a better idea of what is going
on, but don't give up too soon on increasing MAX_ISTACK.


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Received on Tue Feb 22 2005 - 00:53:01 PST
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