AMBER Archive (2003)

Subject: Re: Sander help

From: David A. Case (case_at_scripps.edu)
Date: Tue May 13 2003 - 19:51:12 CDT

On Tue, May 13, 2003, tianxiao yang wrote:
>
> I am moving to run Sander from Amber6 to Amber7 and met big difficulties to
> proceed the calculation. The following is my input file. It is no problem
> to run on V6. But on V7, md.out output file is empty and the error message
> pointed out that there are mistakes in the input file.

First, I'd be curious to know what sort of machine you are running on...I've
never seen completely empty md.out files when there is a mistake in the input.
Where are you getting the error messages from?

Second, you need to post the *exact* error message. Since it "pointed out
that there are mistakes in the input file", are you sure it didn't provide
clues about what those mistakes are?

>
> &cntrl
> imin = 0,
> nsnb = 10, ntpr = 100, ntwx =200, ntwv =100, ntwe =100,
> ntx = 2, irest =0,
> ntc = 2, ntf = 2, ntb = 2,
> nstlim =500000,
> dielc = 1.0,
> ntmin = 1,
> cut = 9.0, nsnb = 10, scee = 1.20,
> ibelly = 0, ntr =1,
> temp0 = 300.0, tempi = 300.0,
> ntt = 1,
> dt = 0.001, t = 0.0, tautp = 0.1,
> ntp = 1, pres0 = 1.0, taup = 0.5, npscal = 1,
> iewald=1,
> &end
> 27.7619180 27.1948140 26.1915520 90.0000000 90.0000000 90.0000000
> 32 32 32 4 0 0 0
> 0.00001
> Hold the solute fixed
> 500
> RES 1
> END
> END
>

The above is *not* a valid input file for sander6; it looks like to me like
you must be back at sander5 or earlier. For example, the "iewald" parameter
doesn't exist at all in amber6 (unless maybe you were running
sander_classic(?), which was essentially from amber5, and was not recommended
for ewald calculations....)

In an event, since you are jumping two versions or so, you just need to
compare the input descriptions with what you have. It looks to me like all
you need to do is remove the "iewald" line, and the three lines that follow
the "&end" line. But it would do no harm to just quickly check that all of
the above variables do what you want them to do.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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