Tarek,
Please resend entire input file. Also please try to create a pdb file
using your parm and coordinate file (ambpdb -p parmtopfile <coordfile>
newpdbfile) . If that fails, you may have an incorrect/corrupt parmtop
file.
Scott
On Thu, 2004-07-22 at 10:59, tarek mahfouz wrote:
> Hi Ross,
> Thanks for our response. I think we have a problem with the amber7
> installed on our unix system.
> We compiled amber7 on a linux machine yesterday (gentoo linux) using
> intel fortran compiler version 8 and we were trying to run the tests.
> Except for different results for energy values from what you got, it
> run ok.
> However, we had the following problem with the ubiquitin and dhfr
> tests. The error message said "non bond list overflow". We decreased
> the cut off value (from 9 to 8) but still the problem exists. Here is
> what the message said:
>
>
> 4. RESULTS
> --------------------------------------------------------------------------------
> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> using 5000.0 points per unit in tabled values
> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
> ---------------------------------------------------
> * NB pairs 916 8243196 exceeds capacity ( 8243681)
> 0
> SIZE OF NONBOND LIST = 8243681
> EWALD BOMB in subroutine ewald_list
> Non bond list overflow!
> check MAXPR in locmem.f
>
> We noticed that the capacity changes as the size of non bond list
> changes so we always get this error.
> So, what would be the parameter to change here?
> Thanks,
> Tarek
>
> Ross Walker <ross.rosswalker.co.uk> wrote:
> Dear Tarek,
>
> There is no format change for the prmtop file between amber 7
> and amber 8. However, there was a change between amber 6 and
> amber 7. Are you certain you are using amber 7?
>
> Also, do you know if you amber 7 installation passes all the
> tests? Can you run other simulations with it?
>
> Did you create the prmtop file yourself following the tutorial
> instructions or did you just download the one that is linked
> to on the website. Have you tried both? Do you get the same
> error message in each case?
>
> A couple of things to try. First of all see if you can read
> the prmtop file with rdparm:
>
> rdparm polyAT_vac.prmtop
>
> look out for any error messages as it loads.
>
> Secondly you could try converting it to an old format prmtop
> file:
>
> new2oldparm < polyAT_vac.prmtop > polyAT_vac.prmtop.old
>
> I have tested the whole tutorial with Amber7 and it all works
> so there must be something wrong with your installation or the
> way your machine has downloaded the prmtop file. Are you on a
> unix machine or a windows machine?
>
> If you can attach the prmtop file you are using to the email
> it would be great.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request
> |
>
>
>
>
> ______________________________________________________
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of tarek
> mahfouz
> Sent: 20 July 2004 12:10
> To: amber.scripps.edu
> Subject: AMBER: Problem with sander tutorial.
>
>
> I'm trying to run the DNA polyAT tutrial (amber 8) and
> I have amber 7 on irix
> but sander is not runing the minimization in. First I
> got an error message about the input file, I changed
> the last line in the input file to end with &end
> statement instead of the /
> Still sander is not runing but this time the error is
> different. This time the message said:
>
>
> fmt: read unexpected character
> apparent state: unit 8 named polyAT_vac.prmtop
> last format: (12I6)
> Unit 8 is a sequential formatted external file
> *** Execution Terminated (115) ***
>
>
> I do not now if there is format change between amber 7
> and 8 in the prmtop file format and so I'm not able to
> solve the problem.
> I'm a new user of amber so please any help will be
> appreciated.
> Thanks,
> Tarek
>
>
> ______________________________________________________________________
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Received on Fri Jul 23 2004 - 03:53:00 PDT
