Hi Maura,
I looked at the topology files, and I saw some weird things at the end.
Residues 201 through 223 are
['LEU', 'GLU', 'VAL', 'ALA', 'GLN', 'THR', 'THR', 'MG1', 'GDP', 'H2O',
'H2O', 'H2O', 'H2O', 'GDP', 'H2O', 'H2O', 'H2O', 'H2O', 'Cl-', 'Cl-', 'Cl-',
'Cl-', 'WAT']
But the ATOMS_PER_MOLECULE of the 2 GDP residues aren't the same (the second
one only says 3!). Furthermore, all of the waters *should* come last in the
residue sequence. Go back to the original PDB files and change all of the
H2O residue names to WAT (or take them out completely if you don't need
them).
Also, if any of the GDP residues are actually bonded covalently to the main
protein anywhere, you should make sure that they come *before* the MG ion in
the PDB.
HTH,
Jason
On Tue, Jun 7, 2011 at 9:08 AM, Jason Swails <jason.swails.gmail.com> wrote:
>
>
> 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
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> > _______________________________________________
>> > 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
>>
>> _______________________________________________
>> 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
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Received on Wed Jun 15 2011 - 14:30:03 PDT
