On Thu, Jun 16, 2011 at 8:54 AM, Maura Catherine Mooney <mmooney05.qub.ac.uk
> wrote:
> Hi Jason,
>
> Without a doubt, I agree with you. However, I wonder...this topology file
> runs with sander (haven't checked the result - but it runs). I have checked
> previous results with this and I don't see anything strange in the
> trajectory. Would you expect to see 2 GDP molecules in the pmemd
> trajectory, or is this just the way pmemd splits the workload. Also,
> running with sander should be ok...right? (not desirable - esp because of
> the speed) Am I right in thinking that sander does not implement
> intermolecular PRFs?
>
All that happened was that there are 2 residues *named* GDP. That doesn't
necessarily mean they are both GDP. You can use a visualization program
(like VMD) to visualize your system, and highlight all resname GDP. This
would show you what's happening. While sander runs without error (since
pmemd and sander arrive at the same answer along 2 completely different
paths). I would take the pmemd error as a warning that you need to fix your
issues with your topology file.
sander does not use PRFs, that's correct. sander splits the workload much
more naively; splitting on actual residues rather than doing any kind of
spatial decomposition with dynamic load balancing like pmemd does (which is
a large part of why it scales so much worse)
> Also, is there any easy way to learn how to read prmtops...is this detailed
> in the manual? I guess a lot of it comes with experience...
>
You can study
http://ambermd.org/formats.html carefully, but as far as I
know it's not detailed in the manual anywhere. That'll give you a *basic*
idea of what each part of the topology file means (but take care to read the
italicized comments!).
Understanding how to actually modify the topology file to get it to do
somewhat more complex things is far more difficult, and requires more time
invested in learning the format, as well as careful study of the codes that
use the topology file. For instance, removing just one water molecule
requires you to adjust just about every section of the topology file (you
have to eliminate the atoms (atom_names, amber_atom_type, atom_type_index,
etc.), adjust the residue_label, residue_pointer, nres, natom, charges,
masses, atoms_per_molecule, solvent_pointers, etc.), and if you mess just
one part up, your prmtop (if you're lucky), will crash pmemd and/or sander
or (if you're unlucky) will run, giving you garbage results without you
knowing.
Even changing the charge of a single atom in the topology file requires you
to remember that each atomic charge is multiplied by 18.223 before being
written to the topology file. As is probably apparent, the topology file
was *not* designed to be human-readable or easily modified.
HTH,
Jason
> Cheers,
>
> Maura.
> ---------------------------------------------------------------
> Maura Mooney
> School of Chemistry and Chemical Engineering
> David Keir Building
> Queens University Belfast
> Stranmillis Road
> Belfast
> BT9 5AG
>
> mmooney05.qub.ac.uk
> mauramooney9.gmail.com
> ________________________________________
> From: Jason Swails [jason.swails.gmail.com]
> Sent: 16 June 2011 15:44
> To: AMBER Mailing List
> Subject: Re: [AMBER] PMEMD does not support intermolecular PRFs
>
> On Thu, Jun 16, 2011 at 8:39 AM, Maura Catherine Mooney <
> mmooney05.qub.ac.uk
> > wrote:
>
> > Hi Prof Case...and Jason,
> >
> > Many Thanx for the speedy reply.
> >
> > >[In general, careful editing of the input pdb file is required for all
> but
> > the
> > >simplest protein or nucleic acid systems, and a careful review of what
> you
> > are
> > >loading is always desirable.]
> >
> > Indeed so, I agree!
> >
> > >Then load your force field and any libraries needed for the GDP or Mg
> > >moieties. Issue a single loadpdb command to create the basic system,
> > >follow this by bond, solvateBox and addIons, etc. as appropriate. Then
> > >examine the prmtop file that is created to make sure you have the
> residues
> > >and ions you want.
> >
> > This is what I have *intended* to do, but obviously, not *exactly* what I
> > did. :) The tutorials are very good for the beginner, where a standard
> > protocol is identified (which is what you mention above). This is what I
> > did, although there were a system-specific tweaks, as always.
> Additionally,
> > I use xleap to prep the inpcrd/prmtop files and always use the 'check'
> > command before creating these files - in your opinion, would you expect
> > xleap 'check' to pick up such errors?
> >
> > FYI, I created this prmtop, using the method you specify above (and that
> > which is detailed in the tutorial). The only difference here is that I
> > implement PM3 qm for the GDP/Mg. ESP charges are calculated in gaussian
> and
> > then the RESP program is used in AMBER. The pdb file is then edited to
> > contain the calculated charges, with a few minor changes (to make the
> system
> > neutral) and resulting lib file is saved. The fact that the prmtop
> *thinks*
> > there are two GDP in the residue labels but only one in the
> > ATOMS_PER_MOLECULE confuses me. Can anything RE the source of the
> problem
> > be taken from this specific info, or is it simply...the topology file is
> > wrong and needs fixed?
> >
> > Finally, the fact that residue labels seems to think there are 2 GDP
> > molecules - is this likely the source of the PMEMD error...I don't know
> > anything about intermolecular PRFs, but think I read that this could be
> due
> > to overlapping atoms. Is this true?
> >
>
> The RESIDUE_LABELs aren't used for anything outside of specifying amber
> mask
> selections and *maybe* some other GB variable initialization. The real
> problem is ATOMS_PER_MOLECULE. When splitting the workload, pmemd is
> assigning 2 different molecules to the same pseudo-residue fragment. In
> particular, RESIDUE_POINTER array shows that the *second* GDP residue is 19
> atoms large, or so, yet ATOMS_PER_MOLECULE will show you that this residue
> is split into several molecules. *This* is probably what I would say is
> causing issues.
>
> Again, your best bet is to get rid of anything weird in your PDB file and
> recreate your topology.
>
> HTH,
> Jason
>
> Many Thanx for the advice.
> >
> > Maura
> > ---------------------------------------------------------------
> > Maura Mooney
> > School of Chemistry and Chemical Engineering
> > David Keir Building
> > Queens University Belfast
> > Stranmillis Road
> > Belfast
> > BT9 5AG
> >
> > mmooney05.qub.ac.uk
> > mauramooney9.gmail.com
> > ________________________________________
> > From: David A Case [case.biomaps.rutgers.edu]
> > Sent: 16 June 2011 15:13
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] PMEMD does not support intermolecular PRFs
> >
> > On Thu, Jun 16, 2011, Maura Catherine Mooney wrote:
> > >
> > > I have little/no experience reading topology files, but I had a look,
> > > based on your response. Strange behaviour indeed, as there is only
> > > *intended* to be one GDP molecule, one Mg and 4 coordinating H2O's.
> >
> > You need to review how you created the topology file in the first place.
> > I recommend creating a single PDB file with exactly what you want in
> > it. Change any H2O or HOH labels to WAT; put a TER card between separate
> > molecules. Remove CONECT records (but be sure to issue a "bond" command
> > later to leap for any disulfide bonds or other non-standard bonds.) It is
> > best to put all the water molecules at the end. If there are alternate
> > conformations in file, choose the one(s) you want and remove the rest.
> >
> > [In general, careful editing of the input pdb file is required for all
> but
> > the
> > simplest protein or nucleic acid systems, and a careful review of what
> you
> > are
> > loading is always desirable.]
> >
> > Then load your force field and any libraries needed for the GDP or Mg
> > moieties. Issue a single loadpdb command to create the basic system,
> > follow this by bond, solvateBox and addIons, etc. as appropriate. Then
> > examine the prmtop file that is created to make sure you have the
> residues
> > and ions you want.
> >
> > ...good luck.....dac
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jun 16 2011 - 19:00:03 PDT
