Re: [AMBER] PMEMD does not support intermolecular PRFs

From: Jason Swails <>
Date: Tue, 7 Jun 2011 01:12:09 -0500

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.


On Mon, Jun 6, 2011 at 10:10 AM, Maura Catherine Mooney <
> 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
> 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 []
> 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
> 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 []
> > Sent: Sunday, June 05, 2011 8:45 AM
> > To:
> > 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
> >
> >
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Jun 06 2011 - 23:30:02 PDT
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