On Tue, Jun 7, 2011 at 6:22 AM, Maura Catherine Mooney
<mmooney05.qub.ac.uk>wrote:
> Hi Jason,
>
> Many Thanx for the reply. I can send you the files to your gmail account
> if that suits? Also, I dont have a script as such for prmtop creation, but
> instead, being relatively new to this, I have just executed the individual
> commands as indicated in the tutorials. I think you are referring to a
> batch script, which carries out all these steps in one. Am I right?
>
For now, how about you just send the prmtop (and yes, to my gmail account).
All the best,
Jason
> Cheers,
>
> Maura
> ________________________________________
> From: Jason Swails [jason.swails.gmail.com]
> Sent: 07 June 2011 07:12
> To: AMBER Mailing List
> Subject: Re: [AMBER] PMEMD does not support intermolecular PRFs
>
> Can you send your topology file as well as all of the files you used to
> create the prmtops?
>
> For instance, I want to be able to run some command like "tleap -f
> your_script" and arrive at the topology file you created.
>
> I'm looking into some weirdness happening in which molecules are not
> properly assigned by leap (but as far as I can tell, this is only with
> funky, user-created library files that I can't quite nail down yet).
>
> I'll be able to tell you if you're seeing a similar problem to the ones
> I've
> been seeing before.
>
> Thanks!
> Jason
>
> On Mon, Jun 6, 2011 at 10:10 AM, Maura Catherine Mooney <
> mmooney05.qub.ac.uk
> > wrote:
>
> > Hi Ross,
> >
> > Many Thanx for the reply. I'll try to explain the prmtop building
> protocol
> > as concisely as possible, then perhaps you can advise where to go next.
> >
> > Firstly, the problem is occurring with two systems; one is the protein in
> > question (X) and the other is the protein in question, complexed to
> another
> > protein (Y). Protein X is available on the PDB and complex (X-Y) is an
> > in-house generated model, using structures from the pdb. Before any work
> > with amber, these 2 systems were prepd and minimized using another
> > commercial software (as AMBER wasn't available at the time). The systems
> in
> > question contain a region which, from the previous protocol, you can see
> > that I intend on studying with QM. According to the tutorial (written by
> > yourself) I have optimized the geometries in gaussian 03 and calculated
> the
> > RESP charges using the resp module (following the same protocol as in the
> > tutorial). This was successful and the respective RESP charges were
> output.
> > The system was then loaded into leap and charges edited for the qm atoms
> in
> > question. Following this, the system was solvated, and neutralized and
> then
> > the lib file was saved. I closed leap, then re-opened and reloaded the
> > files, then used 'check UNIT' to verify the system was ok. After this I
> > saved the prmtop and inpcrd.
> >
> > I'm relatively new to amber to I've no idea the source of this error,
> > however, one thinks it may possibly have something to do with the qm
> system.
> > There is a ligand and an ion in my qm system. For the two systems, each
> qm
> > region contains this ligand and ion, but also a few amino acid
> residues...in
> > system X, I have a lysine residue included (as I thought this would have
> a
> > significant electrostatic contribution), in addition to a Thr residue and
> 4
> > water molecules. In system X-Y, I have the ligand, ion, 4 waters, Thr,
> Lys
> > residue and also, two Asn residues and a charged Asp residue. For the
> > initial G03 GO calculation all residues were included in the qm system,
> and
> > all residues were included in the resp calculation. As I understand,
> when
> > we load xleap, with a forcefield (ff99.SB in my case), xleap will assign
> all
> > standard amino acids with the type/charge as defined in this forcefield.
> In
> > my case, I loaded xleap with the ff99.SB FF but edited the charges to the
> qm
> > region according to my RESP calc output. As you can probably imagine,
> this
> > gave some discrepancy in the neutrality of the system and so I edited the
> > 'truncated' atoms so they were as close to my RESP charges and the
> ff99.SB
> > charges as possible (i've seen simulation output files which 'force
> > neutrality' if there are tiny discrepancies here). My thought process
> > behind this was the fact that upon the lengthy protocol, the charges will
> > undoubtedly fluctuate and so small changes in the truncated qm region
> would
> > be rectified in the subsequent simulations.
> >
> > Only after the resp charges were modified did I solvated, neutrallize and
> > save prmtop and inpcrd files. Is this enough detail to debug this?
> Also, I
> > understand this is a problem relating to system topology, but is the
> actual
> > problem with my system or just the way in which prmtop records the
> topology?
> >
> > Now, for the use of sander...what is pmemd and sander seeing differently
> in
> > the prmtop? Why is it that pmemd doesn't support intermolecular PRFs,
> but
> > assumingly sander does? Also, how reliable is the sander simulation? I
> can
> > use sander to run the NPT equilibration, but is it valid to 'mix and
> match'
> > sander and pmemd, throughout one protocol? FYI, I checked the energies
> of
> > various sander and pmemd simlations and they are similar, so it
> definately
> > implies some sort of coherence.
> >
> > Apologies for the lengthy email and many thanx for the support.
> >
> > P.S I noticed in the amber 11 bugfixes, there is a few issues with the
> CUDA
> > implementation of amber - but I am not using CUDA enabled pmemd, just
> > pmemd.MPI and sander.MPI.
> >
> > Cheers,
> >
> > Maura
> > ________________________________________
> > From: Ross Walker [ross.rosswalker.co.uk]
> > Sent: 06 June 2011 06:12
> > To: 'AMBER Mailing List'
> > Subject: Re: [AMBER] PMEMD does not support intermolecular PRFs
> >
> > Hi Maura,
> >
> > The problem is NOT with your simulation protocol but with your underlying
> > prmtop. PMEMD does not support intermolecular PRF's (for NPT simulations)
> > because you should not be able to build a prmtop file with such a setup.
> So
> > the question is how EXACTLY did you build this prmtop file? - This is
> what
> > we need to debug since leap should not be building such prmtops.
> >
> > A workaround for now is to run the NPT part in sander and then switch to
> > NVT
> > with PMEMD once you have the density equilibrated. Although the correct
> > approach is to figure out how you are building such a system in the first
> > place.
> >
> > All the best
> > Ross
> >
> > > -----Original Message-----
> > > From: Maura Catherine Mooney [mailto:mmooney05.qub.ac.uk]
> > > Sent: Sunday, June 05, 2011 8:45 AM
> > > To: amber.ambermd.org
> > > Subject: [AMBER] PMEMD does not support intermolecular PRFs
> > >
> > > Hi all,
> > >
> > > Perhaps someone could provide some advice on the following issue. I've
> > > only come across one instance of this on the mailing list and, as far
> > > as I can see, the issue wasn't resolved. I'll try to briefly explain.
> > > I'm running some MD simulations. The protocol I'm intending to run is
> > > basically,5000steps solvent restrained minimization,7500steps full
> > > system minimization, 50ps heating MD (classical), 1ns classical
> > > equilibration MD, then switch to qmmm MD for 1ns equilibration and
> > > finally 10ns qmmm production... (equil and prod will be run longer, if
> > > necessary). Using the pmemd module of amber the mini1, mini2 and cmd1
> > > are successful, but the cmd2 fails with error 'PMEMD does not support
> > > intermolecular PRFs'. The issue I read previously on the mailing list
> > > mentioned input problems, but would the problem not arise in either the
> > > mini1, mini2 or cmd1 before this? An interesting point to note is the
> > > fact that this cmd2 job runs using sander. Both pmemd and sander use
> > > the same input files (*.prmtop, *.in and *.inpcrd/*.rst). Also, both
> > > sander and pmemd are run using the *.MPI version.
> > >
> > > Here is the input file for the cmd2 job:
> > >
> > > #title
> > > &cntrl
> > > imin=0, irest=1, ntx=5,
> > > ntb=2, ntp=1,
> > > taup=2.0,
> > > cut =12.0,
> > > ntc=2, ntf=2,
> > > tempi=300.0, temp0=300.00,
> > > ntt=3, gamma_ln=2.0,
> > > nstlim=500000, dt =0.001,
> > > ntpr=5000, ntwx=5000, ntwr=5000,
> > > /
> > >
> > > Is the protocol and input file reasonable? Why does the pmemd job, but
> > > not the sander job fail? If the pmemd job fails, how reliable is the
> > > sander job? Could anyone provide any advice on the pmemd issue, as 1)
> > > my other simulations are run using pmemd, and 2) of, course, we see the
> > > large speed up!
> > >
> > > Thanking you in advance.
> > >
> > > Maura
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
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> >
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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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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> 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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Received on Tue Jun 07 2011 - 08:30:02 PDT
