> From: ross.rosswalker.co.uk> To: amber.scripps.edu> Subject: AMBER: RE: AMBER: about addles:“forrtl: severe (71): integer divide by zero”.> Date: Wed, 14 May 2008 09:30:51 -0700> > >My addles.in is as follow: > >file rprm name=(in.prmtop) read> >file rcrd name=(in.inpcrd) pack=2 read> >file wprm name=(neb.prmtop) wovr> >file wcrd name=(neb.inpcrd) wovr> >action> >~ use original mass> >omas> >pimd> >~ make 30 copies of atom 1 to 22 (the whole system)> >spac numc=30 pick #prt 1 22 done> >*EOD> > I prepared all of the document as the tutorial5. I think there should> be no > >problem. > > > Meanwhile,I repeated the tutorial 5 with deleting the last residue of> the struct1.pdb and struct2. I found >it stopped with the same err:"forrtl:> severe (71): integer divide by zero.''> > If you deleted the last residue then it will no longer have 22 atoms - you> would need to change the addles.in file to reflect the correct number of> atoms which would now be 16 - so #prt 1 22 ----> #p!
rt 1 16> > I am guess the same problem is present with your own system, you have the> number of atoms that addles should copy set incorrectly.> > Good luck,> Ross> > > /\> \/> |\oss Walker> > | Assistant Research Professor |> | San Diego Supercomputer Center |> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk | > | http://www.rosswalker.co.uk | PGP Key available on request |> > Note: Electronic Mail is not secure, has no guarantee of delivery, may not> be read every day, and should not be used for urgent or sensitive issues.
hi，rose
thanks for your explanation of the problem.
I repeated the tutorial 5 deleting the last residue just now,and modifided the number from #prt 1 22
to #prt 1 16. But it did not work all the same. The following is the detail of the err:
AMBER8 Module: addles set up Locally Enhanced Sampling topologyadd_les> file rprm name=(in.prmtop) read The following unit number was assigned 26| New format PARM file being parsed.| Version = 1.000 Date = 05/16/08 Time = 07:47:41 Checking topology sizes against compiled limits Checking topology sizes against compiled limitsadd_les> file rcrd name=(in.inpcrd) pack=2 read The following unit number was assigned 27 urcrd: 27Coordinates only from unit 27 Reading coordinates from input file Reading coordinates from input fileadd_les> file wprm name=(neb.prmtop) wovr The following unit number was assigned 28add_les> file wcrd name=(neb.inpcrd) wovr The following unit number was assigned 29add_les> actionadd_les> ~ use original massadd_les> omas All masses will be left at initial valuesadd_le!
s> pimd writing pimd prmtopadd_les> ~ make 30 copies of atom 1 to 22 (the whole system)add_les> spac numc=30 pick #prt 1 2 done picking from 17 particlesatom, #, orig atom #, copies to make: HH31 1 1 30atom, #, orig atom #, copies to make: CH3 2 2 30 Picked 2 particles Making 30 copiesforrtl: severe (71): integer divide by zeroImage PC Routine Line Source addles 000000000040B9D8 Unknown Unknown Unknownaddles 0000000000406692 Unknown Unknown Unknownaddles 0000000000402F42 Unknown Unknown Unknownlibc.so.6 000000340A81E074 Unknown Unknown Unknownaddles 0000000000402E69 Unknown Unknown Unknown
looking forword for you reply!
xiaobing
2008.5.15
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Received on Sun May 18 2008 - 06:07:16 PDT
