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.ukTo: amber.scripps.eduSubject: 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 PMTo: amber.scripps.eduSubject: 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 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 topolog
y 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 &nbs! p; 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 mas ses will be left at initial valuesadd_les> 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 #, copi!
es to make: CH3 2 2 30 Picked 2 particles Making 30 copiesforrtl: severe (71): integer divide by zeroImage PC Routine &nb! sp; Line Source addles 000000000040B9D8 Unknown Unknown Unknownaddles 0000000000406692 Unknown Unknown Unknownaddles 0000000000402F42 Unknown Unknown Unknownlibc.so.6 000000340A81E074 Unknown &! nbsp; Unknown Unknownaddles &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 - 06:07:41 PDT
