I am copying this to Wei Zhang who put in the addles modifications for NEB,
he may be able to comment more. However, the NEB implementation in AMBER
currently only supports replication of the entire system, I.e. you have to
have the NEB springs on every atom in the simulation. Thus even if you could
create only a partially replicated system in addles it would not work in
sander. Thus at the moment you see the integer divide by zero error whenever
the atoms to replicate do not represent all the atoms in the system.
The error message should probably be made more informative here.
All the best
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
??
Sent: Thursday, May 15, 2008 11:57 PM
To: amber.scripps.edu
Subject: AMBER: RE: AMBER: RE: AMBER: RE: AMBER: RE: AMBER: about addles:
“forrtl: severe (71): integer divide by z
Dear ross
Thanks again for your reply.
I repeat the tutorial 5 with the syntax "#prt 1 17 done" after deleting
the third residue.Everything went smoothly .
But I still have a question is that: is there any wrong I using the
snytax "prt 1 16 done" even useing"prt 1 2 done" ?? Because the pick command
could be used to select any atom which we want to be replicated. Followint
this idea the syntas shoud be right? In fact there always be the report of
err " forrtl: severe (71): integer divide by zero”. And this is really
that I care.
xiaobing
gucas
_____
From: ross.rosswalker.co.uk
To: amber.scripps.edu
Subject: AMBER: RE: AMBER: RE: AMBER: RE: AMBER: about addles:“forrtl:
severe (71): integer divide by zero”.
Date: Thu, 15 May 2008 10:37:22 -0700
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 ooof 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.
h i，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
&nbs! p; The following unit number was assigned 27
urcrd: 27
Coordinates only from unit 27
&nbs! p;
Reading coordinates from input file
&nbs! p; &n bsp;
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 00000000004! 06692 Unknown &nb sp; 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
_____
Windows Live Writer，支持离线撰写博客内容，随时随地想写就写。
<
http://get.live.cn/product/writer.html> 立即使用！
_____
用 Windows Live Spaces 展示个性自我，与好友分享生活！
<
http://spaces.live.com/?page=HP> 了解更多信息！
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun May 18 2008 - 06:07:51 PDT
