Hi Jason,
Thanks a lot, that's very helpful. I got it by ignoring both ligand and
Receptors and Ligands and only calculated the trajectory file as a complex.
As shown on the command line below: the -cp is for the complex prmtop file.
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -cp 50nowat.prmtop -y md1_7nowat.x
-eo energyout285
Again, thanks!
-Binwu
On Sun, Jul 8, 2012 at 3:00 PM, <amber-request.ambermd.org> wrote:
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> Today's Topics:
>
> 1. Fwd: Protein aggregation energy calculation (Binwu Zhao)
> 2. Re: Fwd: Protein aggregation energy calculation (Jason Swails)
> 3. Re: What is the typical stimulation time? (Ross Walker)
> 4. Re: different RMSF between CPU and GPU (Ross Walker)
> 5. Re: NaN with GTX580 pmemd.cuda simulation with and without
> iwrap = 1 (Fabr?cio Bracht)
> 6. I can prepare Na+ parameter files under LEAPRC.CONSTPH. (kurisaki)
> 7. Re: I can prepare Na+ parameter files under LEAPRC.CONSTPH.
> (Jason Swails)
> 8. Re: NaN with GTX580 pmemd.cuda simulation with and without
> iwrap = 1 (Jason Swails)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 7 Jul 2012 17:54:32 -0400
> From: Binwu Zhao <bzhao.ncsu.edu>
> Subject: [AMBER] Fwd: Protein aggregation energy calculation
> To: amber.ambermd.org
> Message-ID:
> <CABNUZL04tBqttjk5ZuQ76WovWR=
> dkRN-Zk9PTmye_fs+2NgNNg.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> ---------- Forwarded message ----------
> From: Binwu Zhao <bzhao.ncsu.edu>
> Date: Sat, Jul 7, 2012 at 5:48 PM
> Subject: Protein aggregation energy calculation
> To: amber.ambermd.org
>
>
> Dear Amber users:
>
> I'm very new to MMPB/GBSA, I was wondering if there is a way to calculate
> the free energy of a single aggregated polypeptide chain. Because that is
> the only chain in my explicit water system. I try to learn MMPBSA's
> protocol, but what comfuses me is that there are always Receptors Ligands
> and Complex three parts. A simple system as mine, what should I do to
> calculate the only energy within the one polypeptide chain?
> I would really appreciate that if somebody could help me out.
>
> -Binwu
>
> --
> Binwu Zhao
> Dept of Chemical and Biomolecular Engineerig
> NCSU
>
>
>
>
> --
> Binwu Zhao
> Dept of Chemical and Biomolecular Engineerig
> NCSU
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 7 Jul 2012 21:50:25 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] Fwd: Protein aggregation energy calculation
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAEk9e3rpsSRwLAmc8yVvusmSp1VHVzJWKeCaXwoKF1+MV74jLw.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello,
>
> There are two main things that MM/PBSA can calculate for you. You can get
> binding free energies (complex, receptor, ligand -- like you pointed out)
> or you can do so-called stability calculations in which there is only one
> system (designated as the 'complex' in MMPBSA.py, but you don't have a
> receptor or ligand).
>
> Stability calculations reveal the relative stabilities of (at least) two
> different structures/conformations.
>
> Ultimately, a single point energy of a single structure is meaningless in
> computational chemistry, since the 'zero' energy is arbitrarily chosen for
> convenience. The only thing that has meaning (i.e., the only thing
> measurable/observable in the lab) is a change in energy. Stability
> calculations gives you the difference in (free) energy of different
> conformations.
>
> You can look at this paper for a good overview of the method:
> http://dx.doi.org/10.1002/minf.201100135
>
> HTH,
> Jason
>
> On Sat, Jul 7, 2012 at 5:54 PM, Binwu Zhao <bzhao.ncsu.edu> wrote:
>
> > ---------- Forwarded message ----------
> > From: Binwu Zhao <bzhao.ncsu.edu>
> > Date: Sat, Jul 7, 2012 at 5:48 PM
> > Subject: Protein aggregation energy calculation
> > To: amber.ambermd.org
> >
> >
> > Dear Amber users:
> >
> > I'm very new to MMPB/GBSA, I was wondering if there is a way to calculate
> > the free energy of a single aggregated polypeptide chain. Because that is
> > the only chain in my explicit water system. I try to learn MMPBSA's
> > protocol, but what comfuses me is that there are always Receptors Ligands
> > and Complex three parts. A simple system as mine, what should I do to
> > calculate the only energy within the one polypeptide chain?
> > I would really appreciate that if somebody could help me out.
> >
> > -Binwu
> >
> > --
> > Binwu Zhao
> > Dept of Chemical and Biomolecular Engineerig
> > NCSU
> >
> >
> >
> >
> > --
> > Binwu Zhao
> > Dept of Chemical and Biomolecular Engineerig
> > NCSU
> > _______________________________________________
> > 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
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 7 Jul 2012 21:19:40 -0700
> From: "Ross Walker" <ross.rosswalker.co.uk>
> Subject: Re: [AMBER] What is the typical stimulation time?
> To: "'AMBER Mailing List'" <amber.ambermd.org>
> Message-ID: <014301cd5cc0$e5cd84e0$b1688ea0$.rosswalker.co.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> > Concerning Ross' 2nd suggestion "Write a simple script that starts with
> > the data for frame 1 and calculates the binding energy, then repeats
> > this for frames 1,2 combined, then 1,2,3, then 1 to 4
> > etc."
> >
> > This seems to me very heavy on computer resources. Am I right?
>
> Not really. Assuming you already have all the data, i.e. the actual
> simulations have been run (and in the example I give the PBSA calcs done)
> then it is really just a case of processing the data multiple times. In the
> case of calculating the binding energy for MMPBSA this should be only a few
> minutes at most on the average desktop.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 7 Jul 2012 21:21:57 -0700
> From: "Ross Walker" <ross.rosswalker.co.uk>
> Subject: Re: [AMBER] different RMSF between CPU and GPU
> To: "'AMBER Mailing List'" <amber.ambermd.org>
> Message-ID: <014401cd5cc1$37519770$a5f4c650$.rosswalker.co.uk>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Massimiliano,
>
> If you used IG=-1 for all simulations then I am a little concerned about
> the
> differences you see. We haven't seen this in our validation so I wonder
> where it is coming from. Can you please send me all of your files (off
> list)
> so I can try to reproduce what you are seeing. I'll keep the files
> confidential.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Massimiliano Porrini [mailto:M.Porrini.ed.ac.uk]
> > Sent: Saturday, July 07, 2012 11:57 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] different RMSF between CPU and GPU
> >
> > Hey Ross,
> >
> > Thanks for the reply.
> >
> > Yup, I was aware that 1 ns simulation is certainly not enough to
> > obtain a satisfactory
> > sampling and convergence.
> > But I was worried because the GPU runs produced practically the same
> > results
> > which, compared with the CPU run, they just appear somehow "scaled":
> > if you look at the graphs I attached in the previous email the trend of
> > the RMSF
> > is in fact the same, but let's say enhanced in the case of the CPU run.
> >
> > By the way, it might depends on, as you say, how the GPU and CPU codes
> > handle
> > the random number seed, which I changed for the production runs by
> > setting
> > ig=-1 (as recommended in Amber tutorials). Here is my dyn.in input file
> > though:
> >
> > dynamics complex
> > &cntrl
> > imin = 0, irest = 1, ntx = 5,
> > nstlim = 500000, dt = 0.002,
> > ntc = 2, ntf = 2,
> > cut = 10.0, ntb = 1,
> > ntpr = 1000, ntwx = 1000,
> > ntt = 3, gamma_ln = 2.0,
> > temp0 = 300.0,
> > ig = -1,
> > iwrap = 1
> > /
> >
> > The version I am using is Amber11 (the one you helped me to install
> > here in Edinburgh :-) ) with all the applied bugfixes described in
> > Jason Swails
> > Wiki page:
> >
> > http://jswails.wikidot.com/installing-amber11-and-ambertools-1-5
> >
> > that is bugfixes till number 20.
> >
> > Anyway I'll try to run the simulations with different random seed and
> > different number of
> > CPUs too.
> >
> > Thanks again.
> > Max
> >
> >
> >
> > 2012/7/6 Ross Walker <ross.rosswalker.co.uk>:
> > > Hi Massimiliano,
> > >
> > >> I was doing some benchmarks on my system using the
> > >> GPU boards I have and the 16 cores CPU of my machine.
> > >>
> > >> After minimising and equilibrating the system, I ran four 1ns
> > >> simulation using:
> > >>
> > >> - 16 cores of my CPU
> > >> - 1 Tesla C2070
> > >> - 2 Teslas C2070
> > >> - 1 GeForce GTX 470
> > >
> > > These results are almost certainly NOT converged. When comparing CPU
> > and GPU
> > > results we have typically run around 50 simulations, each of 100ns
> > and even
> > > then the RMSFs are not fully converged. The GPU runs will all be the
> > same
> > > since that code is deterministic. You don't give your input settings
> > so it
> > > is hard to comment more but for example if you are using NTT=3 the
> > random
> > > number generator on the CPU is different from that used on the 3 GPU
> > runs
> > > which would account for the differences in such short runs.
> > >
> > > I would suggest repeating the GPU runs with different random number
> > seeds
> > > and the same for the 16 cores of the CPU (try 8 cores and 1 core as
> > well for
> > > comparison). I'm betting you'll see differences between individual
> > runs that
> > > are larger than the differences you see here which will give you an
> > idea of
> > > how unconverged the results are.
> > >
> > >> Then, after centering (ptraj center) and re-imaging (ptraj image)
> > and
> > >> aligning (ptraj rms)
> > >> the produced trajectories I have worked out the RMSF and I obtained
> > a
> > >> substantial
> > >> difference between the 16cores CPU trajectory and the GPU ones
> > >> (RMSFs obtained from the 3 different GPU runs are practically the
> > >> same).
> > >
> > > Also what version of the code are you using, which patch level in
> > terms of
> > > bugfixes etc.
> > >
> > >> Any idea on which is the correct one?
> > >
> > > I suspect all of them are correct, and equally incorrect.
> > >
> > > All the best
> > > Ross
> > >
> > > /\
> > > \/
> > > |\oss Walker
> > >
> > > ---------------------------------------------------------
> > > | Assistant Research Professor |
> > > | San Diego Supercomputer Center |
> > > | Adjunct Assistant Professor |
> > > | Dept. of Chemistry and Biochemistry |
> > > | University of California San Diego |
> > > | NVIDIA Fellow |
> > > | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> > > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > > ---------------------------------------------------------
> > >
> > > Note: Electronic Mail is not secure, has no guarantee of delivery,
> > may not
> > > be read every day, and should not be used for urgent or sensitive
> > issues.
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > Dr Massimiliano Porrini
> > Institute for Condensed Matter and Complex Systems
> > School of Physics & Astronomy
> > The University of Edinburgh
> > James Clerk Maxwell Building
> > The King's Buildings
> > Mayfield Road
> > Edinburgh EH9 3JZ
> >
> > Tel +44-(0)131-650-5229
> >
> > E-mails : M.Porrini.ed.ac.uk
> > mozz76.gmail.com
> > maxp.iesl.forth.gr
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Sun, 8 Jul 2012 03:41:35 -0300
> From: Fabr?cio Bracht <bracht.iq.ufrj.br>
> Subject: Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and
> without iwrap = 1
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAMRmCxujJ4ZBPzDL7zbciYxAUPbypHtGztqXKMX9610aB+1Hbw.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> SG ( SH) 5311 ZN ( ZN) 2.3440 73.7200
> ZN ( ZN) 5312 O ( OH) 1.9240 140.4500
> Strangely though, the md methot frcmod file didn't have any bond
> parameters for the O - Ho bond. Do you think it is safe to use the 553
> from the other method?
>
> The thing with the lennard-jones parameters is this. I had written at
> the end of the frcmod file lines containing ljparam for Ho (MCPB had
> already written parameters for sulfur, so, I'm not counting that one).
> When I do the whole leap routine, (loadamberparams myparam.frcmod and
> loadamberprep myprep.prep, etc etc) everything works fine. I set up
> the bonds with the bond command, and finally get my prmtop and inpcrd
> files.
> Once I use xparmed.py to check the prmtop file, I get the info that my
> Ho atom does not have the parameters I have specified for it. It still
> shows up as having 0.000 and 0.000 for well depth and radius. Leap
> does not exit with an error message, and to make sure, I have done the
> whole thing again and got the same thing. I tried also to rename the
> Ho atom (hoping that leap was misunderstanding my Ho for HO, which has
> 0.000 for params), and that didn't work out as well. When I try to
> change the values using "changeLJsingetype" command from parmed.xy, I
> get :
>
> Changing :342.Ho Lennard-Jones well depth from 0.0000 to 0.0300
> (kal/mol) and radius from 0.0000 to 0.2000
>
> But when I ask it to write a new frcmod file (not overwrite the
> previous one, actually write a new. Just in case the overwriting does
> not work), the values are not there. The same thing happens when I ask
> it to write a new prmtop file.
>
> I have not seen any "unexpected" behaviour from leap. Bu then again,
> what do you mean by unexpected behaviour? The only warning I get is
> the no zero charge warning before adding ions.
> Cheers
> Fabr?cio Bracht
>
> 2012/7/7 Ben Roberts <ben.roberts.geek.nz>:
> > Hi Fabr?cio,
> >
> > Hmm. So that says to me that your angle force constants may not be
> strong enough. At least, they aren't managing to counteract the
> electrostatic attraction. Before you start playing with them, though, what
> are the force constants from the "md" (a.k.a. Z-matrix) method, if you
> still have the results from that method? Of course, the other suspect is
> the LJ parameters, for which, read on...
> >
> > As you say, the fact that the Lennard-Jones parameters for the hydrogen
> atom aren't being picked up is concerning. Is it that the Ho type is
> getting incorrect LJ parameters, or is it rather that that particular
> hydrogen atom isn't getting typed correctly? Also, are you sure that the
> inpcrd and prmtop files are being overwritten, that is, that LEaP isn't
> simply exiting with an error and leaving you with the same inpcrd and
> prmtop files that you had previously? Finally, is there anything in
> leap.log that suggests unexpected behaviour?
> >
> > Ben
> >
> > On 7/07/2012, at 5:56 AM, Fabr?cio Bracht wrote:
> >
> >> Here is the information you required:
> >>> - The atomic partial charges of the hydrogen and sulphur atoms
> >> Hydrogen +0.4193
> >> Sulfur -0.6779
> >>> - The Lennard-Jones parameters of those atoms
> >> Hydrogen LJ Radius 0.0000 LJ Depth 0.0000
> >> Sulfur LJ Radius 2.0000 LJ Depth 0.2500
> >>> - The bond parameters of SG-ZN, ZN-O and OH-Ho
> >> Atom 1 Atom 2 R eq Frc Cnst
> >> SG ( SH) 5314 ZN ( ZN) 2.3440 48.9000
> >> ZN ( ZN) 5315 O ( OH) 1.9240 111.6400
> >> O ( OH) 5316 H1 ( Ho) 0.9600 553.0000
> >>> - The angle parameters of SG-ZN-OH and ZN-OH-Ho
> >> Atom 1 Atom 2 Atom 3 Frc
> >> Cnst Theta eq
> >> SG ( SH) 5314 ZN ( ZN) 5315 O ( OH) 36.6440
> 117.1331
> >> ZN ( ZN) 5315 O ( OH) 5316 H1 ( Ho) 16.3980
> 108.0340
> >>> - A list of which particular bonds and angles among these are
> significantly distorted from their reference values (r0 and theta0) as the
> hydrogen and sulphur atoms approach each other
> >> Taking as example the two angle parameters described above, the ZN - O
> >> - H1 angle stays at an approximate value of 70?. As for the SG-ZN-O
> >> the value varies between 70 and 110 staying most of the simulation at
> >> values around 70?. The bond distances do not seem to differ much from
> >> the reference values.
> >>
> >>> - A description of which parameter set you used.
> >> I have used the seminario method to get my parameters.
> >>
> >> One thing should be noted though. I specifically placed the following
> >> lines within my frcmod file:
> >>
> >> NONB
> >> Ho 0.20 0.030
> >>
> >> As I wished to include these lennard jones parameters in order to
> >> overcome the problem I previously had with my simulation crashing.
> >> But, as I can see now from the prmtop file, these parameters are still
> >> not there. I tried then to modify them using xparmed.py by
> >> substituting the lennardjones parameters from these hydrogen atoms,
> >> but the resulting parameter file still showed LJ radius and LJ depth =
> >> 0.0000.
> >> What am I doing wrong? If the parameters were still not included, then
> >> I must be that the error I got with the NaN values were not caused by
> >> these settings, or am I interpreting things in the wrong manner here?
> >> Thank you
> >> Fabr?cio Bracht
> >>
> >> 2012/7/5 Ben Roberts <ben.roberts.geek.nz>:
> >>> Hi Fabr?cio,
> >>>
> >>> The electrostatics and van der Waals parameters can also be obtained
> using rdparm. There's a command one can use (called, I think, "help") that
> prints out a list of commands one can use to get a list of the
> electrostatic and Lennard-Jones parameters.
> >>>
> >>> The torsional parameter you provided removes any remaining doubt in my
> mind that torsions are *not* directly responsible for what you're seeing. I
> had already suspected that was the case. A torsional parameter, being
> solely concerned with rotation around the central bond, should not pull the
> atoms in 1- and 4- positions towards each other, as that would involve a
> force component orthogonal to any "torsional" force.
> >>>
> >>> To the best of my knowledge, attractive forces between two particles,
> of the sort that would cause unusual geometries, could only result from:
> >>>
> >>> - A spurious bond record;
> >>> - A harmonic restraint; or
> >>> - Non-bonding (i.e., electrostatic and/or van der Waals) interactions.
> >>>
> >>> You've already said there is only one bond to that hydrogen, which
> rules out the spurious bond explanation. Likewise, I would guess you aren't
> using any harmonic restraints, though it would be helpful if you could
> confirm that. Which leaves only the non-bonding interactions, that I've
> already alluded to.
> >>>
> >>> Thus, it seems likely to me that you have highly charged particles and
> the combination of van der Waals parameters and bond/angle/torsion
> parameters isn't enough to keep them apart. Given that, perhaps you could
> supply for us more bits of information:
> >>>
> >>> - The atomic partial charges of the hydrogen and sulphur atoms
> >>> - The Lennard-Jones parameters of those atoms
> >>> - The bond parameters of SG-ZN, ZN-OH and OH-Ho
> >>> - The angle parameters of SG-ZN-OH and ZN-OH-Ho
> >>> - A list of which particular bonds and angles among these are
> significantly distorted from their reference values (r0 and theta0) as the
> hydrogen and sulphur atoms approach each other
> >>> - A description of which parameter set you used. Did you make your
> parameters using MCPB? If so, did you use the MD (Z-matrix) method or the
> seminario method to get your parameters? I ask because one of these creates
> overly weak bonds, and the other overly weak angles, so I've found it
> necessary to mix the two in the past.
> >>>
> >>> Cheers,
> >>> Ben
> >>>
> >>> On 6/07/2012, at 8:42 AM, Fabr?cio Bracht wrote:
> >>>
> >>>> Hi Ben. Rdparm shows me that the only bond that exist with this
> >>>> hydrogen is the one I have specified in the frcmod file (with the
> >>>> hydroxyl oxygen). As to the electrostatics and van der Waals, I am not
> >>>> exactly sure where would I obtain that information. Some help on this
> >>>> would be great.
> >>>> The apparent attempt to bond seems more like a very strong hydrogen
> >>>> bond pulling the geometry towards that direction. It would not be what
> >>>> one would expect for many reasons. Chemically speaking, the geometry
> >>>> impediment would huge, since it is trying to from a three membered
> >>>> ring. I've noticed, however, that the columns regarding this
> >>>> particular dihedral angle (SG - ZN - O - Ho), when I ask in rdparm for
> >>>> "dihedral :340.ZN" are like this:
> >>>>
> >>>> Dihedral pk phase pn atoms
> >>>> 1166: 0.000 0.00 3.0 :31.SG :339.ZN :340.O :340.H1
> >>>> (531,5311,5312,5313)
> >>>>
> >>>> Is that normal?
> >>>> Thank you
> >>>> Fabr?cio Bracht
> >>>>
> >>>> 2012/7/4 Ben Roberts <ben.roberts.geek.nz>:
> >>>>> Hi Fabr?cio,
> >>>>>
> >>>>> What does the program "rdparm" show in your topology? Is there any
> indication of a bond record or an angle record between the Ho and SG atoms?
> And are the electrostatics and van der Waals parameters appropriate,
> particularly when scaled to 1-4? And can you describe more of the
> connection between the torsional angle and the apparent attempt to "bond" -
> that is, are the bonds and angles involved chemically sensible?
> >>>>>
> >>>>> Cheers,
> >>>>> Ben
> >>>>>
> >>>>> On 5/07/2012, at 6:20 AM, Fabr?cio Bracht wrote:
> >>>>>
> >>>>>> Hello. I have some interesting news. The procedure of addind the
> >>>>>> glycam vdwradii seems to have solved the problem. I ran 10 ns using
> >>>>>> pmemd.mpi and right after that I ran another 10 ns using pmemd.cuda.
> >>>>>> Although the simulation now proceeds without any error, I have
> notice
> >>>>>> that the dihedral angle for SG-ZN-OH-Ho (the cysteine Sulfur, the
> zinc
> >>>>>> atom, the hydroxyl's oxygen and the hydroxyl's hydrogen) changes
> from
> >>>>>> something around 130?-140? to -145? and than to 15? (more or less).
> >>>>>> The visual aspect of the geometry is of a distorted one (for the
> >>>>>> pmemd.cuda step). It looks as though the hydrogen is trying to bond
> >>>>>> with the cysteine sulfur atom. Any help here would be great.
> >>>>>> Thank you
> >>>>>> Fabr?cio Bracht
> >>>>>>
> >>>>>> 2012/6/28 Fabr?cio Bracht <bracht.iq.ufrj.br>:
> >>>>>>> Hello. Thank you for the advice. I've taken the GLYCAM path.
> Renamed
> >>>>>>> my HO to Ho and started the process again. Will know if it worked
> in a
> >>>>>>> few days. I'll contact the developers of GLYCAM in order to get
> more
> >>>>>>> information, as well as some tips that my help my particular case.
> >>>>>>>
> >>>>>>> Thank you again for all the advice.
> >>>>>>> Fabr?cio Bracht
> >>>>>>>
> >>>>>>> 2012/6/28 Ross Walker <ross.rosswalker.co.uk>:
> >>>>>>>> Hi Fabricio,
> >>>>>>>>
> >>>>>>>> I suggest 'NOT' using parmed in this situation - if you start
> hacking the
> >>>>>>>> prmtop file you will most likely forget what you did, or not
> interpret it
> >>>>>>>> properly and when it comes time to publish and someone asks for
> the force
> >>>>>>>> field parameters file and setup files to reproduce your work you
> won't have
> >>>>>>>> them. Instead I would go back and modify the original
> parameterization files
> >>>>>>>> you used in leap. This way it is clearly documented what you did
> and what
> >>>>>>>> you changed. The hacking approach is useful to quickly test a
> hypothesis but
> >>>>>>>> is no excuse for not being diligent in the approach in the first
> place.
> >>>>>>>>
> >>>>>>>> The VDW Radii do not come from the pdb file. They are VDW
> parameters
> >>>>>>>> specified for the atom type in the parmXX.dat file or frcmod
> file. Here's an
> >>>>>>>> example:
> >>>>>>>>
> >>>>>>>> http://ambermd.org/tutorials/advanced/tutorial1_adv/
> >>>>>>>>
> >>>>>>>> plc.frcmod:
> >>>>>>>>
> >>>>>>>> # modifications to force field for poplar plastocyanin
> >>>>>>>>
> >>>>>>>> MASS
> >>>>>>>> SM 32.06
> >>>>>>>> CU 65.36
> >>>>>>>>
> >>>>>>>> BOND
> >>>>>>>> NB-CU 70.000 2.05000 #kludge by JRS
> >>>>>>>> ...
> >>>>>>>>
> >>>>>>>> ANGLE
> >>>>>>>> CU-NB-CV 50.000 126.700 #JRS estimate
> >>>>>>>> ...
> >>>>>>>>
> >>>>>>>> DIHE
> >>>>>>>> X -NB-CU-X 1 0.000 180.000 3.000
> >>>>>>>> ...
> >>>>>>>>
> >>>>>>>> NONBON
> >>>>>>>> CU 2.20 0.200
> >>>>>>>> SM 2.00 0.200
> >>>>>>>>
> >>>>>>>> The values in the nonbond section correspond to the following:
> >>>>>>>>
> >>>>>>>> LTYNB , R , EDEP
> >>>>>>>>
> >>>>>>>> LTYNB Atom symbol.
> >>>>>>>>
> >>>>>>>> R The van der Waals radius of the atoms having the
> symbol
> >>>>>>>> "LTYNB" (Angstoms)
> >>>>>>>>
> >>>>>>>> EDEP The 6-12 potential well depth. (kcal/mol)
> >>>>>>>>
> >>>>>>>> If you then look at $AMBERHOME/dat/leap/parm/parm99.dat you will
> see:
> >>>>>>>>
> >>>>>>>> H 0.6000 0.0157 !Ferguson base pair geom.
> >>>>>>>> HO 0.0000 0.0000 OPLS Jorgensen,
> >>>>>>>> JACS,110,(1988),1657
> >>>>>>>> HS 0.6000 0.0157 W. Cornell CH3SH --> CH3OH
> FEP
> >>>>>>>>
> >>>>>>>> And there is your problem. The HO has no VDW interaction and thus
> can
> >>>>>>>> collapse on other atoms. It doesn't if it is bonded or angled
> with them
> >>>>>>>> since nonbond interactions are excluded for 1-2 and 1-3 terms but
> if it is a
> >>>>>>>> 1-4 term or a 1-5 term or more than it has a charge interaction
> which could
> >>>>>>>> be strong if they are different signs and pull the HO atom into
> it.
> >>>>>>>>
> >>>>>>>> One approach is what they do for hydroxyl's in Charmm All22:
> >>>>>>>>
> >>>>>>>> !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 -
> 2(Rmin,i,j/ri,j)**6]
> >>>>>>>> !
> >>>>>>>> !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
> >>>>>>>> !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
> >>>>>>>> !
> >>>>>>>> !atom ignored epsilon Rmin/2 ignored eps,1-4
> Rmin/2,1-4
> >>>>>>>> ...
> >>>>>>>> HT 0.000000 -0.046000 0.224500 ! ALLOW WAT
> >>>>>>>>
> >>>>>>>> Or you can look at what they do for GLYCAM_06H which is to define
> a Ho atom
> >>>>>>>> type and give it a small VDW term:
> >>>>>>>>
> >>>>>>>> Ho 0.2000 0.0300 M.B. Tessier 2011, use by
> >>>>>>>> permission only
> >>>>>>>>
> >>>>>>>> This is how they stop the hydroxyl hydrogens collapsing onto
> hydroxyl
> >>>>>>>> oxygens in sugar rings.
> >>>>>>>>
> >>>>>>>> These are both hacks I believe, I don't think they actually
> fitted the
> >>>>>>>> parameters here but you might want to ask the authors of those
> force fields
> >>>>>>>> for details behind it. Then for your system you'll take your
> frcmod file
> >>>>>>>> that you build during the parameterization and also the mol2 file
> (or lib
> >>>>>>>> file) edit the atom types for the hydroxyl's to be something
> unused and then
> >>>>>>>> provide the parameters (mass, bond, angle, dihedral) for this in
> the frcmod
> >>>>>>>> file and finally at the end include the small VDW parameters that
> you want
> >>>>>>>> for that atom.
> >>>>>>>>
> >>>>>>>> Good luck,
> >>>>>>>>
> >>>>>>>> All the best
> >>>>>>>> Ross
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>> -----Original Message-----
> >>>>>>>>> From: Fabr?cio Bracht [mailto:bracht.iq.ufrj.br]
> >>>>>>>>> Sent: Thursday, June 28, 2012 1:29 PM
> >>>>>>>>> To: AMBER Mailing List
> >>>>>>>>> Subject: Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with
> and
> >>>>>>>>> without iwrap = 1
> >>>>>>>>>
> >>>>>>>>> Hello Ross. Thank you for the reply. I?ll restart the
> parameterization
> >>>>>>>>> procedure. You suggest I create a new H type. I understand that
> >>>>>>>>> setting a new type for this hydrogen would require me to include
> >>>>>>>>> vdwradii for this atom. The problem is that I am not sure how I
> would
> >>>>>>>>> do this. I would just have to rename the pdb source file? But
> then,
> >>>>>>>>> how would I set the vdwradii? Can?t I just set the vdwradii for
> this
> >>>>>>>>> particular atom in tleap, after having performed the
> parameterization?
> >>>>>>>>> Wouldn?t the lmodprmtop program be of use in this case?.
> >>>>>>>>> Thank you in advance
> >>>>>>>>> Fabr?cio Bracht
> >>>>>>>>>
> >>>>>>>>> 2012/6/28 Ross Walker <ross.rosswalker.co.uk>:
> >>>>>>>>>> Hi Fabricio,
> >>>>>>>>>>
> >>>>>>>>>> So you are running into one of the problems with the AMBER force
> >>>>>>>>> field that
> >>>>>>>>>> people have ignored for years and it was never too much of a
> problem
> >>>>>>>>> since
> >>>>>>>>>> people didn't typically run for long enough to see it. That is
> that
> >>>>>>>>> hydroxyl
> >>>>>>>>>> hydrogens have a zero VDW radii. In TIP3P water this is not a
> problem
> >>>>>>>>>> because it is rigid and the H sits inside the VDW radii of the
> >>>>>>>>> oxygen.
> >>>>>>>>>> However, when you start moving to highly charged systems, a
> classic
> >>>>>>>>> example
> >>>>>>>>>> being phosphates you can end up with the H collapsing into one
> of the
> >>>>>>>>> other
> >>>>>>>>>> negatively charged atoms for which there is not a bond or angle
> term
> >>>>>>>>> to
> >>>>>>>>>> prevent it and as soon as that distance becomes very small so
> you
> >>>>>>>>> divide by
> >>>>>>>>>> zero and get NAN. The CPU is a little more tolerant of division
> by
> >>>>>>>>> VERY
> >>>>>>>>>> small numbers than the GPU and that's why it manifests itself
> more as
> >>>>>>>>> a blow
> >>>>>>>>>> up (trapped by vlimit) on the CPU and you get NAN on the GPU.
> Either
> >>>>>>>>> way the
> >>>>>>>>>> simulation is bust because this event is non physical. 1fs can
> help,
> >>>>>>>>> since
> >>>>>>>>>> the thing won't shoot off as much but it still won't really fix
> the
> >>>>>>>>> problem.
> >>>>>>>>>>
> >>>>>>>>>> I would take a VERY careful look at the parameterization - that
> is
> >>>>>>>>> the
> >>>>>>>>>> underlying problem. To begin with you probably should not use
> type HO
> >>>>>>>>> for
> >>>>>>>>>> the hydrogen and instead create a new type. Then make sure this
> new H
> >>>>>>>>> type
> >>>>>>>>>> has at least a small VDW radii, a very small radii will help
> (look in
> >>>>>>>>> the
> >>>>>>>>>> frcmod file) but ideally one should probably attempt to refit
> the
> >>>>>>>>> radii
> >>>>>>>>>> properly for such cases but this is tricky. In your case I
> would just
> >>>>>>>>> put a
> >>>>>>>>>> small radii on the hydrogen (take a look at what the charmm
> people do
> >>>>>>>>> with
> >>>>>>>>>> TIP3P - which in charmm should really strictly be called
> TIP3P-CHARMM
> >>>>>>>>> since
> >>>>>>>>>> it isn't the original TIP3P parameterization due to the
> addition of
> >>>>>>>>> small
> >>>>>>>>>> radii on the hydroxyl hydrogens.)
> >>>>>>>>>>
> >>>>>>>>>> What this does highlight though is that it is important that
> people
> >>>>>>>>> still
> >>>>>>>>>> test things on the CPU and not just rely on the GPU code for
> >>>>>>>>> everything. If
> >>>>>>>>>> you see a problem with a GPU run then switch to CPU and analyse
> >>>>>>>>> things
> >>>>>>>>>> carefully. Don't expect the CPU code to also explode since it
> is more
> >>>>>>>>>> tolerant of marginal stability cases but at least be aware that
> you
> >>>>>>>>> might be
> >>>>>>>>>> simulating something that is borderline stable at best.
> >>>>>>>>>>
> >>>>>>>>>> All the best
> >>>>>>>>>> Ross
> >>>>>>>>>>
> >>>>>>>>>>> -----Original Message-----
> >>>>>>>>>>> From: Fabr?cio Bracht [mailto:bracht.iq.ufrj.br]
> >>>>>>>>>>> Sent: Thursday, June 28, 2012 12:09 PM
> >>>>>>>>>>> To: AMBER Mailing List
> >>>>>>>>>>> Subject: Re: [AMBER] NaN with GTX580 pmemd.cuda simulation
> with and
> >>>>>>>>>>> without iwrap = 1
> >>>>>>>>>>>
> >>>>>>>>>>> Hello. Thank you for the reply. In fact, a time step of 1fs
> seems to
> >>>>>>>>>>> work around the problem. At the same time as i was writing the
> last
> >>>>>>>>>>> email, I had submitted a job with dt = 0.001 and it finished
> without
> >>>>>>>>>>> any problems. I haven?t tested yet with pmemd.cuda, but I?ll
> do that
> >>>>>>>>>>> later on.
> >>>>>>>>>>> The two atoms involved in this case are O and H of the hydroxyl
> >>>>>>>>>>> residue linked to the zinc atom of the active site. Where do I
> find
> >>>>>>>>>>> the Lennard-Jones rmin values for them? The hole active site
> was
> >>>>>>>>>>> parameterized following the steps on the MTK++ manual.
> >>>>>>>>>>> I?ll follow your instructions as to getting a restart file
> from a
> >>>>>>>>>>> previous step and test it out. I?ll inform you as soon as I
> have the
> >>>>>>>>>>> results.
> >>>>>>>>>>> Thank you
> >>>>>>>>>>> Fabr?cio Bracht
> >>>>>>>>>>>
> >>>>>>>>>>> 2012/6/28 David A Case <case.biomaps.rutgers.edu>:
> >>>>>>>>>>>> On Thu, Jun 28, 2012, Fabr?cio Bracht wrote:
> >>>>>>>>>>>>
> >>>>>>>>>>>>> Hi. I did what you asked. I ran the simulation again, in
> order to
> >>>>>>>>>>> make
> >>>>>>>>>>>>> sure that the error happened again. This time, it dies a lot
> >>>>>>>>> earlier
> >>>>>>>>>>>>> with the same warnings as last time (vlimit exceed....etc). I
> >>>>>>>>>>>>> continued the simulation using as input the last restrt file
> >>>>>>>>> written
> >>>>>>>>>>>>> using the serial version of pmemd. The simulation crashed
> after a
> >>>>>>>>>>> few
> >>>>>>>>>>>>> hours , the last output lines are:
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> vlimit exceeded for step 112126; vmax = 91.1788
> >>>>>>>>>>>>> vlimit exceeded for step 112176; vmax = 45.6806
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> Coordinate resetting cannot be accomplished,
> >>>>>>>>>>>>> deviation is too large
> >>>>>>>>>>>>> iter_cnt, my_bond_idx, i and j are
> >>>>>>>>>>> : 2 2690 5315 5316
> >>>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> Thanks for the info. It looks to me like the problem has
> nothing
> >>>>>>>>> to
> >>>>>>>>>>> do (per
> >>>>>>>>>>>> se) with GPU's, since you can reproduce it on a serial CPU
> using
> >>>>>>>>>>> pmemd.
> >>>>>>>>>>>> Unfortuantely, problems like this (generally with the force
> field)
> >>>>>>>>>>> can be hard
> >>>>>>>>>>>> to track down. Your mdin file looks fine to me, although it
> is
> >>>>>>>>> safer
> >>>>>>>>>>> to use
> >>>>>>>>>>>> dt=0.001 rather than 0.002, especially for constant pressure
> >>>>>>>>>>> simulations, and
> >>>>>>>>>>>> if you system is not *quite* equilibrated.
> >>>>>>>>>>>>
> >>>>>>>>>>>> The information above indicates that the problem occurs around
> >>>>>>>>> atoms
> >>>>>>>>>>> 5315
> >>>>>>>>>>>> and 5316. You might see what those are, as this might (or
> might
> >>>>>>>>> not)
> >>>>>>>>>>> give
> >>>>>>>>>>>> a clue to the origin of the problem. Look hard (and/or let us
> >>>>>>>>> know
> >>>>>>>>>>> about)
> >>>>>>>>>>>> any non-standard residues or molecules that are in your
> >>>>>>>>>>> simulation. Do
> >>>>>>>>>>>> you have any Lennard-Jones rmin values that are either zero or
> >>>>>>>>> small
> >>>>>>>>>>> (i.e.
> >>>>>>>>>>>> less than typical values for that type of atom)? You may
> have to
> >>>>>>>>> get
> >>>>>>>>>>> a
> >>>>>>>>>>>> restart file someplace a little before step 112126; (don't use
> >>>>>>>>> ig=-1
> >>>>>>>>>>> to do
> >>>>>>>>>>>> this: copy the actual seed that is printed in your output
> file, so
> >>>>>>>>>>> you will
> >>>>>>>>>>>> get an identical trajectory.) Then you can set ntwx=1, and
> >>>>>>>>> examine
> >>>>>>>>>>> the
> >>>>>>>>>>>> coordinates at every step as the system crashes....one hopes
> that
> >>>>>>>>>>> this will
> >>>>>>>>>>>> identify the source of the problem.
> >>>>>>>>>>>>
> >>>>>>>>>>>> ...good luck...dac
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>> 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
> >>>>>>>>>
> >>>>>>>>> _______________________________________________
> >>>>>>>>> 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
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> 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
> >>
> >> _______________________________________________
> >> 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
>
>
>
> ------------------------------
>
> Message: 6
> Date: Sun, 8 Jul 2012 17:22:39 +0900
> From: "kurisaki" <kurisaki.ncube.human.nagoya-u.ac.jp>
> Subject: [AMBER] I can prepare Na+ parameter files under
> LEAPRC.CONSTPH.
> To: "'AMBER Mailing List'" <amber.ambermd.org>
> Message-ID: <000001cd5ce2$d69f97c0$83dec740$.human.nagoya-u.ac.jp>
> Content-Type: text/plain; charset="iso-2022-jp"
>
> Dear Amber developers and users,
>
> Thank you for usual kind support.
>
> I am now trying to perform constant pH
> MD.
> ?leaprc.constph? was loaded in LEaP
> and
> I just tried to save the parameter
> files.
>
> As the messages say, this leaprc file
> includes
> Several ions but the warning was
> returned.
>
> (The messages are shown below)
>
> ?Loading parameters:
> /home/kurisaki/amber/amber12/dat/leap/pa
> rm/parm10.dat
> ?Reading title:
> ?PARM99 + frcmod.ff99SB +
> frcmod.parmbsc0 + OL3 for RNA
> ?Loading library:
> /home/kurisaki/amber/amber12/dat/leap/li
> b/amino10.lib
> ?Loading library:
> /home/kurisaki/amber/amber12/dat/leap/li
> b/aminoct10.lib
> ?Loading library:
> /home/kurisaki/amber/amber12/dat/leap/li
> b/aminont10.lib
> ?Loading library:
> /home/kurisaki/amber/amber12/dat/leap/li
> b/phosphoaa10.lib
> ?Loading library:
> /home/kurisaki/amber/amber12/dat/leap/li
> b/nucleic10.lib
> ?Loading library:
> /home/kurisaki/amber/amber12/dat/leap/li
> b/ions08.lib
> ?Loading library:
> /home/kurisaki/amber/amber12/dat/leap/li
> b/solvents.lib
> ?Loading library:
> /home/kurisaki/amber/amber12/dat/leap/li
> b/constph.lib
> ?Loading library:
> /home/kurisaki/amber/amber12/dat/leap/li
> b/all_prot_nucleic10.lib
> ?Loading library:
> /home/kurisaki/amber/amber12/dat/leap/li
> b/cph_nucleic_caps.lib
> ?Loading parameters:
> /home/kurisaki/amber/amber12/dat/leap/pa
> rm/frcmod.constph
> ?Reading force field modification type
> file (frcmod)
> ?Reading title:
> ?Force field modifcations for
> titrations
> ?Loading parameters:
> /home/kurisaki/amber/amber12/dat/leap/pa
> rm/frcmod.protonated_nucleic
> ?Reading force field modification type
> file (frcmod)
> ?Reading title:
> ?Force field modifications for
> protonated nucleic acids
> ?Using H(N)-modified Bondi radii
>
> ?Loading PDB file: ./test.pdb
> total atoms in file: 4726
> ? Leap added 5 missing atoms according
> to residue templates:
> ? 5 H / lone pairs
> ?Checking Unit.
> ?WARNING: The unperturbed charge of the
> unit: 5.000000 is not zero.
>
> ? -- ignoring the warning.
>
> ?Building topology.
> ?Building atom parameters.
> ?For atom: .R<Na+ 296>.A<Na+ 1> Could
> not find type: Na+
> ?Parameter file was not saved.
> ? Quit
>
> (END)
>
> This situation was not improved by
> Loading leaprc.ff99SB, additionally.
>
>
> I am most grateful if you tell me how to
>
> Resolve this discrepancy.
>
> Yours, sincerely.
>
> Ikuo
> Kurisaki
>
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Sun, 8 Jul 2012 12:09:02 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] I can prepare Na+ parameter files under
> LEAPRC.CONSTPH.
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAEk9e3o2pU7edpGpMncFz2htXULstO6uaTo8d-fUHowx8gtZFA.mail.gmail.com>
> Content-Type: text/plain; charset=windows-1252
>
> Ion parameters are now loaded separately, since the "correct" parameters
> depend on the water model you're using. You will need to load the frcmod
> file "frcmod.ionsjc_{water model}" where {water model} is tip3p, spce, or
> tip4pew.
>
> However, constant pH simulations only work currently in implicit solvent,
> and ions are not used in implicit solvent simulations. As a result, you
> should not add ions to your system. Ion effects are modelled via a
> Debye-Huckel screening parameter added to the GB model (via the saltcon
> input variable).
>
> This is a helpful thread here: http://archive.ambermd.org/201206/0313.html
>
> HTH,
> Jason
>
> On Sun, Jul 8, 2012 at 4:22 AM, kurisaki <
> kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
>
> > Dear Amber developers and users,
> >
> > Thank you for usual kind support.
> >
> > I am now trying to perform constant pH
> > MD.
> > ?leaprc.constph? was loaded in LEaP
> > and
> > I just tried to save the parameter
> > files.
> >
> > As the messages say, this leaprc file
> > includes
> > Several ions but the warning was
> > returned.
> >
> > (The messages are shown below)
> >
> > Loading parameters:
> > /home/kurisaki/amber/amber12/dat/leap/pa
> > rm/parm10.dat
> > Reading title:
> > PARM99 + frcmod.ff99SB +
> > frcmod.parmbsc0 + OL3 for RNA
> > Loading library:
> > /home/kurisaki/amber/amber12/dat/leap/li
> > b/amino10.lib
> > Loading library:
> > /home/kurisaki/amber/amber12/dat/leap/li
> > b/aminoct10.lib
> > Loading library:
> > /home/kurisaki/amber/amber12/dat/leap/li
> > b/aminont10.lib
> > Loading library:
> > /home/kurisaki/amber/amber12/dat/leap/li
> > b/phosphoaa10.lib
> > Loading library:
> > /home/kurisaki/amber/amber12/dat/leap/li
> > b/nucleic10.lib
> > Loading library:
> > /home/kurisaki/amber/amber12/dat/leap/li
> > b/ions08.lib
> > Loading library:
> > /home/kurisaki/amber/amber12/dat/leap/li
> > b/solvents.lib
> > Loading library:
> > /home/kurisaki/amber/amber12/dat/leap/li
> > b/constph.lib
> > Loading library:
> > /home/kurisaki/amber/amber12/dat/leap/li
> > b/all_prot_nucleic10.lib
> > Loading library:
> > /home/kurisaki/amber/amber12/dat/leap/li
> > b/cph_nucleic_caps.lib
> > Loading parameters:
> > /home/kurisaki/amber/amber12/dat/leap/pa
> > rm/frcmod.constph
> > Reading force field modification type
> > file (frcmod)
> > Reading title:
> > Force field modifcations for
> > titrations
> > Loading parameters:
> > /home/kurisaki/amber/amber12/dat/leap/pa
> > rm/frcmod.protonated_nucleic
> > Reading force field modification type
> > file (frcmod)
> > Reading title:
> > Force field modifications for
> > protonated nucleic acids
> > Using H(N)-modified Bondi radii
> >
> > Loading PDB file: ./test.pdb
> > total atoms in file: 4726
> > Leap added 5 missing atoms according
> > to residue templates:
> > 5 H / lone pairs
> > Checking Unit.
> > WARNING: The unperturbed charge of the
> > unit: 5.000000 is not zero.
> >
> > -- ignoring the warning.
> >
> > Building topology.
> > Building atom parameters.
> > For atom: .R<Na+ 296>.A<Na+ 1> Could
> > not find type: Na+
> > Parameter file was not saved.
> > Quit
> >
> > (END)
> >
> > This situation was not improved by
> > Loading leaprc.ff99SB, additionally.
> >
> >
> > I am most grateful if you tell me how to
> >
> > Resolve this discrepancy.
> >
> > Yours, sincerely.
> >
> > Ikuo
> > Kurisaki
> >
> >
> >
> > _______________________________________________
> > 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
>
>
> ------------------------------
>
> Message: 8
> Date: Sun, 8 Jul 2012 13:46:53 -0400
> From: Jason Swails <jason.swails.gmail.com>
> Subject: Re: [AMBER] NaN with GTX580 pmemd.cuda simulation with and
> without iwrap = 1
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <
> CAEk9e3qMzkmJk0YLN1cbP-EDepJrb2eaU-3ygQCg_Dk9LhuDhA.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Sun, Jul 8, 2012 at 2:41 AM, Fabr?cio Bracht <bracht.iq.ufrj.br> wrote:
>
> > SG ( SH) 5311 ZN ( ZN) 2.3440 73.7200
> > ZN ( ZN) 5312 O ( OH) 1.9240 140.4500
> > Strangely though, the md methot frcmod file didn't have any bond
> > parameters for the O - Ho bond. Do you think it is safe to use the 553
> > from the other method?
> >
> > The thing with the lennard-jones parameters is this. I had written at
> > the end of the frcmod file lines containing ljparam for Ho (MCPB had
> > already written parameters for sulfur, so, I'm not counting that one).
> > When I do the whole leap routine, (loadamberparams myparam.frcmod and
> > loadamberprep myprep.prep, etc etc) everything works fine. I set up
> > the bonds with the bond command, and finally get my prmtop and inpcrd
> > files.
> > Once I use xparmed.py to check the prmtop file, I get the info that my
> > Ho atom does not have the parameters I have specified for it. It still
> > shows up as having 0.000 and 0.000 for well depth and radius. Leap
> > does not exit with an error message, and to make sure, I have done the
> > whole thing again and got the same thing. I tried also to rename the
> > Ho atom (hoping that leap was misunderstanding my Ho for HO, which has
> > 0.000 for params), and that didn't work out as well. When I try to
> > change the values using "changeLJsingetype" command from parmed.xy, I
> > get :
> >
> > Changing :342.Ho Lennard-Jones well depth from 0.0000 to 0.0300
> > (kal/mol) and radius from 0.0000 to 0.2000
> >
>
> I can verify that this does not work as expected. (A problem being that
> None and 0 both evaluate to logical False in Python, so this is a special
> case). I will release a patch for this shortly.
>
> Thanks!
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
>
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>
> End of AMBER Digest, Vol 207, Issue 1
> *************************************
>
--
Binwu Zhao
Dept of Chemical and Biomolecular Engineerig
NCSU
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Received on Thu Jul 12 2012 - 11:30:03 PDT
