[gmx-users] crash in gromacs-4.0.2 using vsites and 2fs t.s.

[gportel]

Hi everyone,

I'm having problems running an md simulation (with gmx-4.0.2) using vsites
and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem
seems to occur when the molecule crosses pbc, since the first sign of the
simulation not working fine after ~3ns is

"
Warning: 1-4 interaction between 6 and 8 at distance 6.122 which is larger
than the 1-4 table size 2.400 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
"

where 6 and 8 are connected via a bond. After that, several lincs warnings
are displayed, plus water molecules not being able to be settled. It ends
up crashing due to errors in the domain decomposition

"
-909 particles communicated to PME node 0 are more than a cell length out
of the domain decomposition cell of their charge group
"

although I'm positive this is the consequence of all I described above.

This might be the relevant part of my mdp,

integrator   = md
dt   = 0.004
nsteps   = 5000
nstlist  = 10
ns-type  = Grid
pbc  = xyz
rlist= 1.4
coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.4
vdw-type = shift
rvdw-switch  = 0.8
rvdw = 1.2
fourierspacing   = 0.14
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 3d
Tcoupl   = v-rescale
tc_grps  = system
tau_t= 0.1
ref_t= 300.00
Pcoupl   = Berendsen
Pcoupltype   = isotropic
tau_p= 1.0
compressibility  = 4.5e-5
ref_p= 1.0
constraints  = all-bonds
constraint-algorithm = Lincs
lincs-order  =  6
lincs-iter   = 2
lincs-warnangle  = 30


I've tried, perhaps naively, using both options for periodic_molecule with
the same results.

I guess it's hard to tell what did go wrong, but perhaps somebody has an
idea.. I thought of submitting a bugzilla, but maybe there are some more
tests I could do to pin point the problem before. Any ideas?


All the best,


Guillem

Dr. Guillem Portella
MMB - Institute for Research in Biomedicine
Parc Cientific de Barcelona
http://mmb.pcb.ub.es/~gportella









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[gmx-users] (no subject)

[gportel]

Justin A. Lemkul wrote:
>
>
> [EMAIL PROTECTED] wrote:
>>
>> Hi everyone,
>>
>> I'm having problems running an md simulation (with gmx-4.0.2) using vsites
>> and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem
>> seems to occur when the molecule crosses pbc, since the first sign of the
>> simulation not working fine after ~3ns is
>>
>> "
>> Warning: 1-4 interaction between 6 and 8 at distance 6.122 which is larger
>> than the 1-4 table size 2.400 nm
>> These are ignored for the rest of the simulation
>> This usually means your system is exploding,
>> if not, you should increase table-extension in your mdp file
>> or with user tables increase the table size
>> "
>>
>
> This is a commonly reported problem.  See here:
>
> http://wiki.gromacs.org/index.php/blowing_up
>

Thanks, I was aware of this entry in the wiki.

> Also search the list archives; you will pull up several hundred posts
describing the problems other users have faced and how they overcame
them.
>

> Other things that would be helpful to know if you are still having
problems: What does your system contain?  Did it adequately minimize? 
What kind of equilibration procedure did you perform?

It's dna, ions and water. After I placed the appropriate entries in the
ddb and bonded itp, I was checking whether I could go for 4fs, and I
prepared different runs with different time steps. The set-ups that made
the simulation crash were the ones where the dna had the time/chance to
cross pbc. If this did not occur, the simulation went fine (i.e. did not
explode). Also, in the mean time I run a simulation in NVE with the same
settings and I did no observe the crash after 5ns, despite having jumps
over the pbc in the last few hundreds of ps.

I energy minimized the system with steepest descend, repeated a couple of
times. They went fine after some initial lincs warnings. I admit I did not
equilibrate much, however the crash happens after more than 3ns... let's
consider the first 2ns some sort of tempering.

Although my nstxtcout was set low enough to resolve the frames just before
the crash, I strongly suspect it has to do with crossing the pbc I
will run a couple of simulations with output freq. 1 and double check.


>
> 
>
>> Tcoupl   = v-rescale
>> tc_grps  = system
>> tau_t= 0.1
>> ref_t= 300.00
>
> Maybe you want "Protein Non-Protein" instead of "system" here?  But
that's just general advice, without any knowledge of what's in your
system.
>


Right, although I don't think this is the problem. Just wanted to see if
the sim. would run fine for some ns before production runs. Just occured
to me now, I will also try with the old berendsen, just to double check,
since I did not have any problem in NVE.

> -Justin

Thanks for your time!

Guillem

>
>> Pcoupl   = Berendsen
>> Pcoupltype   = isotropic
>> tau_p= 1.0
>> compressibility  = 4.5e-5
>> ref_p= 1.0
>> constraints  = all-bonds
>> constraint-algorithm = Lincs
>> lincs-order  =  6
>> lincs-iter   = 2
>> lincs-warnangle  = 30
>>
>>
>> I've tried, perhaps naively, using both options for periodic_molecule with
>> the same results.
>>
>> I guess it's hard to tell what did go wrong, but perhaps somebody has an
>> idea.. I thought of submitting a bugzilla, but maybe there are some more
>> tests I could do to pin point the problem before. Any ideas?
>>
>>
>> All the best,
>>
>>
>> Guillem
>>
>> Dr. Guillem Portella
>> MMB - Institute for Research in Biomedicine
>> Parc Cientific de Barcelona
>> http://mmb.pcb.ub.es/~gportella
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
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>>
>

-- 
Dr. Guillem Portella
MMB - Institute for Research in Biomedicine
Parc Cientific de Barcelona
http://mmb.pcb.ub.es/~gportella


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Re: [gmx-users] crash in gromacs-4.0.2 using vsites and 2fs t.s.

[gportel]

--- Missatge original 
Assumpte:
De:   [EMAIL PROTECTED]
Data: Tue, Novembre 25, 2008 9:52 am
A:"Discussion list for GROMACS users" 
  [EMAIL PROTECTED]
--


ps, I forgot the Subject in the mail!


Justin A. Lemkul wrote:
>
>
> [EMAIL PROTECTED] wrote:
>>
>> Hi everyone,
>>
>> I'm having problems running an md simulation (with gmx-4.0.2) using vsites
>> and a time step of 4fs. I did generate the tpr with pdb2gmx. The problem
>> seems to occur when the molecule crosses pbc, since the first sign of the
>> simulation not working fine after ~3ns is
>>
>> "
>> Warning: 1-4 interaction between 6 and 8 at distance 6.122 which is larger
>> than the 1-4 table size 2.400 nm
>> These are ignored for the rest of the simulation
>> This usually means your system is exploding,
>> if not, you should increase table-extension in your mdp file
>> or with user tables increase the table size
>> "
>>
>
> This is a commonly reported problem.  See here:
>
> http://wiki.gromacs.org/index.php/blowing_up
>

Thanks, I was aware of this entry in the wiki.

> Also search the list archives; you will pull up several hundred posts
describing the problems other users have faced and how they overcame
them.
>

> Other things that would be helpful to know if you are still having
problems: What does your system contain?  Did it adequately minimize?
What kind of equilibration procedure did you perform?

It's dna, ions and water. After I placed the appropriate entries in the
ddb and bonded itp, I was checking whether I could go for 4fs, and I
prepared different runs with different time steps. The set-ups that made
the simulation crash were the ones where the dna had the time/chance to
cross pbc. If this did not occur, the simulation went fine (i.e. did not
explode). Also, in the mean time I run a simulation in NVE with the same
settings and I did no observe the crash after 5ns, despite having jumps
over the pbc in the last few hundreds of ps.

I energy minimized the system with steepest descend, repeated a couple of
times. They went fine after some initial lincs warnings. I admit I did not
equilibrate much, however the crash happens after more than 3ns... let's
consider the first 2ns some sort of tempering.

Although my nstxtcout was set low enough to resolve the frames just before
the crash, I strongly suspect it has to do with crossing the pbc I
will run a couple of simulations with output freq. 1 and double check.


>
> 
>
>> Tcoupl   = v-rescale
>> tc_grps  = system
>> tau_t= 0.1
>> ref_t= 300.00
>
> Maybe you want "Protein Non-Protein" instead of "system" here?  But
that's just general advice, without any knowledge of what's in your
system.
>


Right, although I don't think this is the problem. Just wanted to see if
the sim. would run fine for some ns before production runs. Just occured
to me now, I will also try with the old berendsen, just to double check,
since I did not have any problem in NVE.

> -Justin

Thanks for your time!

Guillem

>
>> Pcoupl   = Berendsen
>> Pcoupltype   = isotropic
>> tau_p= 1.0
>> compressibility  = 4.5e-5
>> ref_p= 1.0
>> constraints  = all-bonds
>> constraint-algorithm = Lincs
>> lincs-order  =  6
>> lincs-iter   = 2
>> lincs-warnangle  = 30
>>
>>
>> I've tried, perhaps naively, using both options for periodic_molecule with
>> the same results.
>>
>> I guess it's hard to tell what did go wrong, but perhaps somebody has an
>> idea.. I thought of submitting a bugzilla, but maybe there are some more
>> tests I could do to pin point the problem before. Any ideas?
>>
>>
>> All the best,
>>
>>
>> Guillem
>>
>> Dr. Guillem Portella
>> MMB - Institute for Research in Biomedicine
>> Parc Cientific de Barcelona
>> http://mmb.pcb.ub.es/~gportella
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [EMAIL PROTECTED]
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>

-- 
Dr. Guillem Portella
MMB - Institute for Research in Biomedicine
Parc Cientific de Barcelona
http://mmb.pcb.ub.es/~gportella



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Re: [gmx-users] crash in gromacs-4.0.2 using vsites and 2fs t.s.

[gportel]

Hi everyone,

As I wrote yesterday, I'm having problems running stable simulations with
vsites and constraints in all bonds in different time-steps using
gmx-4.0.2. As long as the dna strand does not cross pbc, the simulations
run fine (the longest I did was 5ns). The dna topology was generated with
pdb2gmx, several details on how the simulations were carried out are
listed in the quoted mails below. I also using -dlb auto, just in case it
matters.

I reproduced the crash in two different machines, different starting and
simulations conditions (rectangular or octahedric boxes, Berendsen and
v-rescale, the two options for periodic_molecule). As I reported before,
it happens when pbc are crossed, this time I'm really sure: I resolved the
steps right before the crash time step by time step, plus the distance
separating the 1-4 interactions (the first warning I get before the crash)
is around the length of the corresponding box vector.

In my first round of attempts I did not observe any crash in these systems
in NPE simulations (before I said NVE, but I do have pressure control)
regardless of pbc crossings. I'm running now tests in this ensemble to see
if I can also reproduce the 'non-crashing' behavior. Problem is, at the
moment, that the dna is cooling down and it does not move much from the
box center :-(, so after 4ns it did not cross any box boundary.


Does anybody have a clue of what can be the problem? Or how to debug it in
a more efficient manner? I'm trying to give the information I suspect
could be useful to narrow it down. I can provide more details, data, input
files, etc...

Thanks for your help!

Guillem

Justin A. Lemkul wrote:
> >
> >
> > [EMAIL PROTECTED] wrote:
>> >>
>> >> Hi everyone,
>> >>
>> >> I'm having problems running an md simulation (with gmx-4.0.2) using
vsites
>> >> and a time step of 4fs. I did generate the tpr with pdb2gmx. The
problem
>> >> seems to occur when the molecule crosses pbc, since the first sign
of the
>> >> simulation not working fine after ~3ns is
>> >>
>> >> "
>> >> Warning: 1-4 interaction between 6 and 8 at distance 6.122 which is
larger
>> >> than the 1-4 table size 2.400 nm
>> >> These are ignored for the rest of the simulation
>> >> This usually means your system is exploding,
>> >> if not, you should increase table-extension in your mdp file or with
user tables increase the table size
>> >> "
>> >>
> >
> > This is a commonly reported problem.  See here:
> >
> > http://wiki.gromacs.org/index.php/blowing_up
> >

Thanks, I was aware of this entry in the wiki.

> > Also search the list archives; you will pull up several hundred posts
describing the problems other users have faced and how they overcame them.
> >

> > Other things that would be helpful to know if you are still having
problems: What does your system contain?  Did it adequately minimize? What
kind of equilibration procedure did you perform?

It's dna, ions and water. After I placed the appropriate entries in the
ddb and bonded itp, I was checking whether I could go for 4fs, and I
prepared different runs with different time steps. The set-ups that made
the simulation crash were the ones where the dna had the time/chance to
cross pbc. If this did not occur, the simulation went fine (i.e. did not
explode). Also, in the mean time I run a simulation in NVE with the same
settings and I did no observe the crash after 5ns, despite having jumps
over the pbc in the last few hundreds of ps.

I energy minimized the system with steepest descend, repeated a couple of
times. They went fine after some initial lincs warnings. I admit I did not
equilibrate much, however the crash happens after more than 3ns... let's
consider the first 2ns some sort of tempering.

Although my nstxtcout was set low enough to resolve the frames just before
the crash, I strongly suspect it has to do with crossing the pbc I
will run a couple of simulations with output freq. 1 and double check.


> >
> > 
> >
>> >> Tcoupl   = v-rescale
>> >> tc_grps  = system
>> >> tau_t= 0.1
>> >> ref_t= 300.00
> >
> > Maybe you want "Protein Non-Protein" instead of "system" here?  But
that's just general advice, without any knowledge of what's in your system.
> >


Right, although I don't think this is the problem. Just wanted to see if
the sim. would run fine for some ns before production runs. Just occured
to me now, I will also try with the old berendsen, just to double check,
since I did not have any problem in NVE.

> > -Justin

Thanks for your time!

Guillem

> >
>> >> Pcoupl   = Berendsen
>> >> Pcoupltype   = isotropic
>> >> tau_p= 1.0
>> >> compressibility  = 4.5e-5
>> >> ref_p= 1.0
>> >> constraints  = all-bonds
>> >> constraint-algorithm = Lincs
>> >> lincs-order  =  6
>> >> lincs-iter   = 2
>> >> lincs-warnangle  = 30
>> >>
>> >>
>> >> I've tried

[gmx-users] restarting REMD checkpoint gmx-cvs

[gportel]

Hi users,

I would like to restart some REMD simulations done with the cvs code with
the new checkpoint feature,  but I'm unsure if I'm doing it right. Each
replica has its own state#.cpt file, but it seems to me that the -cpi
option of the cvs mdrun (at version 3.3.99_development_20080718) only
allows one checkpoint file. Is that enough for a correct restart? I did
some tests, and it does restart the dynamics, however I'm not sure if it's
done ok. Why then, do we get a checkpoint file for each replica?


Best,

Guillem

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Re: [gmx-users] converting parmbsc0 dihedrals to RB function

[gportel]

Hi,

Right, the only dihedral angles that do not allow an exact translation to
RB because of the phase are the ones involving the new parametrization for
nucleic acids. Namely, it corrects the alpha/gamma transitions to get the
populations of states right, thus avoiding the loss of helicity on the
long run. For proteins, there's no difference at all, so you can use
ffamber.

I've used the combined approach you mention without problems. The only
thing is that I do not use pdb2gmx. Rather I use amber's tools
(leap+libraries, all free in ambertools) to get a topology, and then I use
a slightly modified version of amb2gmx.pl script to get a gromacs
topology. I only convert the new parmbsc0 dihedrals to type 1 if the phase
does not allow a direct conversion to RB form. Typically you have three
entries for the same dihedral, this is no problem at the itp level, grompp
captures them all. With this approach I reproduced a torsional scan of
parmbsc0 from amber md tool using gromacs, so I feel confident about it.

Another option is to use the ffamber parameters and change the itp file
including the new ones.

I should also mention that I had problems importing the new dihedrals
using pdb2gmx. IIRC, pdb2gmx will only use one definition for dihedral if
type 1 or 3 is used. There was a new dihedral type that could be used in
the development versions, but... for a reason it did not work out for me,
don't recall exactly why. It could well be that it would have worked with
more patience from my side.

Hope this helped, somehow. You were on the right direction anyway.

best,

Guillem


Mark Abraham wrote:
> On 8/04/2010 10:32 PM, Vigneshwar Ramakrishnan wrote:
>> Dear Dr. Mark,
>>
>> Thanks very much for pointing out that GROMACS can handle multiple
>> instances of the parameters with different n for a single dihedral.
>
> I hope I'm right there. There's been discussion on such topics before.
There's some subtle difference between [ dihedrals ] and [ dihedraltypes
] which eludes my memory, but which will be in the archives.
>
>> However, given that, in the existing ffamber ports in GROMACS  the other
>> dihedral parameters have been converted to RB form, would it make a
>> difference to just import these new parameters in the non-RB form?
>
> It will make no numerical difference, but g_energy will probably report
the contribution from the two different functional forms separately.
Attempting to mix *non-bonded* interactions in this kind of way asks for
trouble, because the maths is not well-defined. Here, you're fine,
because the maths is right.
>
>> To my knowledge, the torsional term should not vary (or, vary within
>> acceptable limits) irrespective of the functional form used to calculate
>> it. But I would like to know if there could be some reason for which
>> this assumption cannot be made.
>
> The R-B form might be more efficient to evaluate than a sum of simple
dihedrals in the cases where the angle is zero or 180, which might
explain the ffamber practice.
>
> Mark
>
>> Dear Dr. Alan,
>>
>> Thanks very much for pointing out to the acpypi code. I was able to
>> better understand the conversion procedure.
>>
>> Sincerely,
>> Vignesh
>>
>> On Wed, Apr 7, 2010 at 10:04 PM, Mark Abraham > > wrote:
>>
>> On 7/04/2010 7:44 PM, Vigneshwar Ramakrishnan wrote:
>>
>> Dear Users,
>>
>> I am trying to port the new parmbsc0 forcefield
>> (http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0) into gromacs
for DNA
>> simulations.
>>
>> While unit conversions are sufficient to convert many of the
>> parameters
>> from AMBER to GROMACS format, dihedral angle conversion does not
>> seem to
>> be straight forward - the dihedral parameters need to be
>> converted to
>> the Ryckaert-Bellemans parameters.
>>
>>
>> Why? GROMACS can probably do the non-RB form - IIRC you can
>> implement a sum of multiple instances of 4.61 with different n.
>>
>>
>> I went through the GROMACS 4.0
>> manual, especially equations 4.61-4.65 to understand the
>> procedure. The
>> procedure involves comparing the fourier expansion of the IUPAC
>> convention of dihedral potential (equation 4.65) with the
>> Ryckaert-Bellemans (RB) functional of dihedral potential
>> (equation 4.62)
>> to get the Cn's of the RB function. However, I am not able to
>> understand
>> how to account for the phase angles. (Also to note, the parmbsc0
>> forcefield contains phase angles other than 0 and 180.)
>>
>>
>> Elegant conversion formulae require those angles to be convenient...
>>
>> Mark
>>
>>
>>   Any advice or suggestion will be of great help.
>>
>> Thank you,
>>



Dr. Guillem Portella
- MMB - Institute for Research in Biomedicine
- Parc Cientific de Barcelona -
http://mmb.pcb.ub.es/~gportella



-- 
gmx-users mailing listgmx-users@grom

[gmx-users] Re: converting parmbsc0 dihedrals to RB function

[gportel]

Hi Alan,

I have no experience with acpypi, so I can't tell which one does better,
or why... rdparm not being needed, that would be a strong point.

Unfortunately, I'm running a bit short of time at the moment, so I can't
really spend a lot of time looking into unknown codes, hope you
understand... Nevertheless, the modifications are straightforward : if the
phase of the dihedral in question is different than 0 or 180, then you
should print the 3 dihedrals as type 1 - and converting the units -,
instead of combining them as RB. I did not do anything else to amb2gmx.

best of luck,

Guillem


Alan wrote:
> Hi Guillem,
>
> Many thanks for your clarification. I was lazy to find out and remember
why psc0 was not ported to GMX by ffAmber previously and it was exactly
because what you've said.
>
> And because I was not confident enough, I didn't implement that for
acpypi, which I believe does better than amb2gmx in general, so I would
be glad if you could take a look at it and if you could let me know
which modifications you did to amb2gmx.
>
> I am taking plunge in this problem again and I'll try to come out with a
solution based in what you suggest.
>
> Cheers,
>
> Alan
>
> On Fri, Apr 9, 2010 at 00:53,  wrote:
>
> Right, the only dihedral angles that do not allow an exact
translation to
> RB because of the phase are the ones involving the new
parametrization for
> nucleic acids. Namely, it corrects the alpha/gamma transitions to
get the
> populations of states right, thus avoiding the loss of helicity on the
> long run. For proteins, there's no difference at all, so you can use
> ffamber.
>
> I've used the combined approach you mention without problems. The only
> thing is that I do not use pdb2gmx. Rather I use amber's tools
> (leap+libraries, all free in ambertools) to get a topology, and then
I use
> a slightly modified version of amb2gmx.pl script to get a gromacs
> topology. I only convert the new parmbsc0 dihedrals to type 1 if the
phase
> does not allow a direct conversion to RB form. Typically you have three
> entries for the same dihedral, this is no problem at the itp level,
grompp
> captures them all. With this approach I reproduced a torsional scan of
> parmbsc0 from amber md tool using gromacs, so I feel confident about
it.
>
> Another option is to use the ffamber parameters and change the itp file
> including the new ones.
>
> I should also mention that I had problems importing the new dihedrals
> using pdb2gmx. IIRC, pdb2gmx will only use one definition for
dihedral if
> type 1 or 3 is used. There was a new dihedral type that could be
used in
> the development versions, but... for a reason it did not work out
for me,
> don't recall exactly why. It could well be that it would have worked
with
> more patience from my side.
>
> Hope this helped, somehow. You were on the right direction anyway.
>
> best,
>
> Guillem



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Re: [gmx-users] protein in hole

[gportel]

Hi,

Use editconf. You can center the protein and align its main axis ( -princ
) or play around with the rotation of the initial orientation ( -rotate ).
Then get the surface of the correct (aligned and centered) oritentation as
input for making the hole (if you want to use the modified md code).

Good luck,

Guillem


-

Guillem Portella
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11
D-37077 Göttingen
Germany


>  Dear all
> i want to insert potassium channel in popc, i made
> popc+hole by make-hole but i can not to insert protein
> in popc, i merg the coordinates of the protein and the
> lipid bilayer in a single file, the protein turns out
> not to be inside the hole. I  have to orient the
> protein so that the channel axis coincides with the
> membrane normal.how can i do it by editconf or grasp?
> thanks
>
>
>
>
>
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Re: [gmx-users] g_wham and PMF problem

[gportel]

In the old version of gmx, and I think nobody changed a single line of
code, this is the message you would get regardless of the file you input.
Buggy, yes. Check the mailing list, check the code yourself, as you love
to say.

Guillem

>
>> Opening file pull1.pdo.gz.
>> ---
>> Program g_wham, VERSION 3.3.1
>> Source code file: gmx_wham.c, line: 90
>>
>> Fatal error:
>> This does not appear to be a valid pdo file
>> ---
>> That is the error which I get
>
> So do you know that it *is* a valid .pdo file? Check the file format and
> look at the file yourself :-)
>
> Mark
>
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