Thanks for your reply. Here are the answers to your
questions:
1) All of the Amber tests were passed.
2) specs of my machine:
processor - 24 & 64 bit Opteron 2.0 GHz
compiler - PGI Fortran 5.1
operating system - linux-2.4
3) sequence of steps:
-------------------------------------------------------$AMBERHOME/exe/xleap
-s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
model = loadpdb "nuc_ter.pdb"
saveamberparm model polyAT_vac.prmtop
polyAT_vac.inpcrd
addions model Na+ 0
saveamberparm model polyAT_cio.prmtop
polyAT_cio.inpcrd
solvatebox model TIP3PBOX 8.0
-------------------------------------------------------
Observations:
For the addions command, the output printed on the
xleap window is identical to that in the tutorial, but
when I check the file polyAT_cio.inpcrd, the y and z
coordinates of the ions are all zero.
For the solvatebox command, the output in the xleap
window is:
> solvatebox model TIP3PBOX 8.0
Solute vdw bounding box: 25.736 23.718
40.240
Total bounding box for atom centers: 41.736 39.718
56.240
Solvent unit box: 18.774 18.774
18.774
Total vdw box size: 44.537 23.718
70.662 angstroms.
Volume: 74643.684 A^3
Total mass 77428.892 amu, Density 1.723 g/cc
Added 3940 residues.
while the output in the tutorial is:
> solvatebox model TIP3PBOX 8.0
Solute vdw bounding box: 25.736 26.736
40.240
Total bounding box for atom centers: 41.736 42.736
56.240
Solvent unit box: 18.774 18.774
18.774
Total vdw box size: 44.537 45.963
58.910 angstroms.
Volume: 120593.276 A^3
Total mass 53972.060 amu, Density 0.743 g/cc
Added 2638 residues.
--- Ross Walker <ross.rosswalker.co.uk> wrote:
> Dear Dwayne,
>
> > I am following the instructions given in the DNA
> > tutorial using Amber 8 in linux. The problem I am
> > having is that the solvatebox command puts waters
> only
> > at the end of the DNA structure rather than all
> around
> > it. Also, the addions command only puts ions on
> the x
> > - axis in the .inpcrd file. How can one correct
> this?
>
> This sounds like a possible bug, probably related to
> the compiler used.
>
> Can you:
>
> 1) See if all the amber8 test cases in
> $AMEBRHOME/test work correctly.
>
> 2) Let me know the specs of your machine: cpu, OS,
> compiler versions etc.
> Also if you can post your config.h file from you
> $AMBERHOME/src dir that
> would be useful.
>
> 3) Let me know the exact sequence of commands you
> are using. From initially
> firing up leap to solvating it and finding out it
> has solvated incorrectly.
>
> Hopefully with this information we can nail down
> your problem.
>
> 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 |
>
> 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.
>
>
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Received on Mon Feb 21 2005 - 20:53:00 PST
