That’s because there are 17 atoms in the file when you strip the last
residue since leap converts the ALA to a C terminal residue and adds an
extra oxygen – I should have realized this when I looked at the PDB
although really I think you should have been able to work this out for
yourself, especially since once you actually run it through leap it prints a
message about adding the extra heavy atom.
I just tried it on my machine with prt 1 17 and it works fine.
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
??
Sent: Wednesday, May 14, 2008 5:18 PM
To: amber.scripps.edu
Subject: AMBER: RE: AMBER: RE: AMBER: about addles:“forrtl: severe (71):
integer divide by zero”.
> 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 di! vide 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 ----> #prt 1 16
>
> I am guess the same problem is present with your own system, you have the
> number oof 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 topology
add_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 limits
add_les> file rcrd name=(in.inpcrd) pack=2 read
The following unit number was assigned 27
urcrd: 27
Coordinates only from unit 27
&nbs! p;
Reading coordinates from input file
Reading coordinates from input file
add_les> file wprm name=(neb.prmtop) wovr
The following unit number was assigned 28
add_les> file wcrd name=(neb.inpcrd) wovr
The following unit number was assigned 29
add_les> actionadd_les> ~ use original mass
add_les> omas
All mas ses will be left at initial values
add_les> pimd
writing pimd prmtop
add_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 particles
atom, #, orig atom #, copies to make: HH31 1 1 30
atom, #, orig atom #, copies to make: CH3 2 2 30
Picked 2 particles
Making 30 copies
forrtl: severe (71): integer divide by zero
Image PC Routine &nb! sp; Line
Source
addles 000000000040B9D8 Unknown Unknown Unknown
addles 0000000000406692 Unknown Unknown Unknown
addles 0000000000402F42 Unknown Unknown Unknown
libc.so.6 000000340A81E074 Unknown &! nbsp; Unknown
Unknown
addles &nb sp; 0000000000402E69 Unknown Unknown
Unknown
looking forword for you reply!
xiaobing
2008.5.15
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Received on Sun May 18 2008 - 06:07:31 PDT
