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?
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...
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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>
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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 - 08:00:07 PDT
