AMBER Archive (2000)

Subject: Re: your mail

From: jim caldwell (caldwell_at_heimdal.compchem.ucsf.edu)
Date: Wed Nov 01 2000 - 13:17:25 CST

You didn't "saveamberparmpol" in leap.

On Wed, 1 Nov 2000, Alessandra Ricca wrote:

>
>
> Dear Amber users,
> I have run a sander calculation with the option ipol=1.
> The calculation stops with the following error message:
>
> s_rsfe: end of file -1
> apparent state: unit 8 named polbox.top
> last format: (5E16.8)
> Unit 8 is a sequential formatted external file
> *** Execution Terminated (-1) ***
>
>
> The sander input file is the following:
>
> md, nvt, 300K 50 ps, ipol=1
> &cntrl
> timlim = 99999999., IREST = 0, IMIN = 0, NTX = 1,
> IDIEL = 1, NRUN = 1, NSTLIM = 50000, IPOL = 1,
> TEMPI = 300.0, TEMP0 = 300.0,
> NTT = 1, NTB = 1, NTP = 0,
> NSNB = 25, CUT = 8.000, SCEE = 1.2,
> NTPR = 10,
> NTC = 2, NTF = 2,
> NTWX = 50, NTWE = 100,
> &end
>
>
> I have used the frcmod file kindly provided by Jim Caldwell to
> build the topology file for the pol3 box:
>
> forces for lp's
> MASS
> OW 16.00 0.528
> HW 1.00 0.170
>
> NONB
> OW 1.798 0.156
> HW 0.0 0.0
>
> BOND
> OW-HW 320. 1.0
> HW-HW 553.0 1.6333
>
>
> The pol3 topology file ends like this:
>
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3 3 3 3 3 3 3 3 3 3
> 3 3 3
> 9.00000000E+01 1.92321282E+01 2.66682748E+01 2.51720000E+01
>
> It looks like something is missing at the end of the topology file
> (the polarizabilities I suppose). How can I get the sander calc
> to run ?
>
> Thanks for your help.
>
>
> Alessandra
>
>
>

----------------------------------------------------------------------------
James W. Caldwell (voice) 415-476-8603
Department of Pharmaceutical Chemistry (fax) 415-502-1411
Mail Stop 0446 (email) caldwell_at_heimdal.ucsf.edu
513 Parnassus Avenue (video) farbauti.compchem.ucsf.edu
University of California (netmeeting)
San Francisco, CA 94143-0446
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