[gmx-users] Re: gmx-users Digest, Vol 31, Issue 23
Mauricio Sica
msica at unq.edu.ar
Tue Nov 7 14:57:10 CET 2006
> Hey all
>
> I'm trying to do a simple FEP within a simple protein, which seems to
> make things simple...but as you may expect...it is anything else than
> that.
>
> What I'm trying to do is morphing a Tyrosine into a Phenylalanine in
> OPLSAA.
> Therefore the CZ is changed from the type of TYR to the type of PHE.
> The oxygen(TYR) is changed to a proton(PHE) and the proton(TYR) to a
> dummy (PHE). So this is very simple. We checked the tpr-dump and
> everything looks fine (except, maybe, we missed it). Now, in the
> position-restraint run (where state B should not be regarded by the
> system), the OH-proton moves on top of the OH-oxygen and the simulation
> crashes after a while. We then performed a FEP from TYR to TYR (so A-
> and B-state are the same) and the system runs.
The OH-proton seems to be constrained to the CZ of the aromatic ring, so
it ocupies its proper position when moves on top of the OH-oxygen. It
shoud be contrained to the "new" HZ. See Pearlman JMB (1995) 248, 696-717
> The whole thing was done with GROMACS 3.3.1 and TIP4P. Any suggestions?
> Gerrit and me think of a bug somewhere.
>
> Regards
>
> --
> Maik Goette, Dipl. Biol.
> Max Planck Institute for Biophysical Chemistry
> Theoretical & computational biophysics department
> Am Fassberg 11
> 37077 Goettingen
> Germany
> Tel. : ++49 551 201 2310
> Fax : ++49 551 201 2302
> Email : mgoette[at]mpi-bpc.mpg.de
> mgoette2[at]gwdg.de
> WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 7 Nov 2006 14:31:21 +0100
> From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] invalid order of directive moleule type
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <8ff898150611070531x70ddaacenccf5f5c1ef5ea0d7 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Harpreet,
>
> Regarding the message "invalid order ...", check the archives of this
> mailing list. Further note that you shouldn't use the gmx (ffgmx)
> force field, but should choose one of the Gromos force fields (united
> atom), OPLS or Encad (all-atom).
>
> Specific to your problem is that there is a mismatch between the names
> of atoms in the .pdb file and the names in the residue database (.rtp)
> file of the force field you chose. Usually, it's best to modify the
> names in the .pdb file to match those in the .rtp file.
>
> By the way, since you're new to Gromacs.., have you tried the
> MD/Gromacs tutorial from the MD group in Groningen? If not, it may be
> a good start to get to know gromacs. At present the Groningen group is
> off the air, but I've mirrored the site at:
>
> http://nmr.chem.uu.nl/~tsjerk/MDCourse/
>
> Hope it helps,
>
> Tsjerk
>
> On 11/7/06, merc mertens <merc.mertens at gmx.net> wrote:
> > if i were you, i would rather adapt my pdb file to an existing
> forcefield as ffgmx, than trying to generate a new forcefield that fits
> to your pdb with prodrug. the first option seems much easier to me.
> what i mean is, if you change the names of you FAD atoms to the ones
> you see in the *rtp they will be recognized by pdb2gmx.
> >
> > -------- Original-Nachricht --------
> > Datum: Tue, 07 Nov 2006 11:35:47 +0000
> > Von: "harpreet singh" <harpreetsingh05 at hotmail.com>
> > An: gmx-users at gromacs.org
> > Betreff: [gmx-users] invalid order of directive moleule type
> >
> > > Hi All,
> > > I am new to this package and want your help. I am trying to use
> GROMACS to
> > > study energy minimization and molecular dynamics for FAD molecule.
> I am
> > > having the following problems.
> > > 1. I tried to run pdb2gmx for PDB file for FAD downloaded from
> > > http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl site. and used
> the
> > > gromacs force field . The program gave the following error: -
> > > Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.hdb
> > > Opening library file
> /usr/local/gromacs/share/gromacs/top/ffgmx-n.tdb
> > > Opening library file
> /usr/local/gromacs/share/gromacs/top/ffgmx-c.tdb
> > >
> > > Back Off! I just backed up fad_test.top to ./#fad_test.top.1#
> > > Processing chain 1 (53 atoms, 1 residues)
> > > There are 0 donors and 0 acceptors
> > > There are 0 hydrogen bonds
> > > -------------------------------------------------------
> > > Program pdb2gmx, VERSION 3.3.1
> > > Source code file: pdb2gmx.c, line: 393
> > > Fatal error:
> > > Atom O1P in residue FAD 1 not found in rtp entry with 61 atoms
> > > while sorting atoms
> > > On comparing topology file (ffgmx.rtp) for FAD entry i was surpried
> to see
> > > that it has atom type enteries OP1, OP2 instead of O1P, O2P in
> downloaded
> > > PDB file (fad.pdb). Also atom type at number 23 was O in ffgmx.rtp
> (for
> > > FAD) and O3P was missing in this file. I am attaching the files
> herewith.
> > >
> > > 2. I tried to make .top and .gro files (fad92.top and fad.gro
> > > respectively)
> > > ,using PRODRG2 server. and used them with grompp commad
> > >
> > > grompp -f em.mdp -c fad92.gro -p fad92.top -o fad92.tpr
> > >
> > > This resulted in the following error.
> > >
> > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
> > > checking input for internal consistency...
> > > calling /usr/bin/cpp...
> > > processing topology...
> > > Cleaning up temporary file gromppfYcUxi
> > > -------------------------------------------------------
> > > Program grompp, VERSION 3.3.1
> > > Source code file: topio.c, line: 388
> > >
> > > Fatal error:
> > > Invalid order for directive moleculetype, file ""fad92.top"", line
> 15
> > > -------------------------------------------------------
> > >
> > > "Oh, There Goes Gravity" (Eminem)
> > >
> > > Kindly guide me to solve this problem.
> > > Thanks in advance
> > >
> > > Harpreet Singh
> > >
> > > _________________________________________________________________
> > > Use your PC to make calls at very low rates
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> > >
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> post-doc
> NMR, Utrecht University,
> Padualaan 8,
> 3584 CH Utrecht, the Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
>
> ------------------------------
>
> Message: 6
> Date: Tue, 07 Nov 2006 10:31:34 -0300
> From: "Mauricio Sica" <msica at unq.edu.ar>
> Subject: [gmx-users] Re: Re: (dH/dl) calculation
> To: gmx-users at gromacs.org
> Message-ID: <WorldClient-F200611071031.AA31341148 at unq.edu.ar>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Tanks David
>
> Exactly: I`d want to calculate "dG/dl for some particular component of
> the energy". Why? I did 2 FEPs, so I have two Delta_Gs for a mutations
> in
> 2 states: folded and unfolded. Both Delta_Gs are positive values. The
> difference between them (Delta_Delta_G) is the value I was looking for.
> This value agrees with experimental value of Delta_G of unfolding
> between
> 2 mutant proteins. Now, I want to know what is stabilizing or
> destabilizing each state with respect the other. Analysis of each
> component (e.g. Coul-SR:Prot-Prot) is impossible: it happens that I’m
> searching a delta_E of < 10 Kcal between a magnitude of 10E6. So I
> thought that if I could obtain a <dE/dl> for a component and then
> integrate them along lambda (TI method), I could get some idea about
> its
> magnitude.
>
> Mauricio
>
> > Mauricio,
> >
> > > That was exactly what I wanted to know. From one hand, because I
> just
> > > wanted to know it and, from the other hand, because I think that if
> I
> > have
> > > some idea about how this calculus is carried out, I was able to
> > estimate a
> > > Delta_E for some energy components, for example,
> > Coul-SR:Protein-Protein
> > > by means of calculating the corresponding <dE/dl> (even when I know
> > that
> > > the value is not a state function as stated in the Mark & v
> Gunsteren
> > > paper). Maybe I should have started from this point. Is it posible?
> >
> > I'm sorry, I have no idea what you're asking here. Are you talking
> > about trying to calculate a dG/dl for some particular component of
> the
> > energy? That doesn't sound useful, to me, since the components
> > generally are all interdependent. And if you are trying to separate
> > out the contribution of different components to the total dG/dl, this
> > would require source code modifications, in general. Again, if you
> can
> > be more specific about what exactly you want to do (what problem are
> > you trying to solve?) people may be able to be more helpful.
> >
> > David
> >
> >
> > > > Message: 6
> > > > Date: Mon, 6 Nov 2006 10:19:05 -0800
> > >
> > > > Mauricio,
> > > >
> > > > I'm somewhat confused by your question and notation. However, I
> > think
> > > > the basic answer is something like this: In molecular dynamics,
> you
> > > > know the Hamiltonian from which you are sampling; call it H(x,p,
> > l),
> > > > where x denotes all of the positions, p the momentums, and l
> > lambda.
> > > > This, of course, is closely linked to the potential energy.
> Anyway,
> > at
> > > > any snapshot, you can simply take the derivative dH(x,p,l)/dl,
> and
> > you
> > > > have dH/dl at that snapshot. This is usually straightforward
> since
> > you
> > > > know the dependence of all of the terms in your Hamiltonian on
> > lambda,
> > > > so you actually have the functional form for dH/dl as well -- so
> it
> > > > just involves taking the appropriate combination of positions,
> > > > momentums, etc. This is of course all handled internally by the
> > code.
> > > > <dH/dl>, then, is just the time-average of dH/dl, which can be
> > > > evaluated every step by the code.
> > > >
> > > > I am not sure if that's helpful at all, as I'm not entirely sure
> > what
> > > > problem you're having. After all, whenever you do TI calculations
> > in
> > > > GROMACS, the code gives you back dG/dl (or dH/dl, or dA/dl) for
> > every
> > > > snapshot in an xvg output file. Are you just confused about how
> the
> > > > code gets this (I think I just answered that above), or are you
> > trying
> > > > to figure out how to use it? If you're confused about how to use
> > it,
> > > > try to ask a question that relates to the specific issue you're
> > > > confused about.
> > > >
> > > > Best wishes,
> > > > David Mobley
> > > > UCSF
> > > >
> > > >
> > > > On 11/5/06, Mauricio Sica <msica at unq.edu.ar> wrote:
> > > > > Dear experts
> > > > >
> > > > > I am doing FEP (thermodynamic integration method) simulations.
> > > > > I have a questions about <dH/dl> calculation in GROMACS.
> > > > > Take in mind equation 3.77 from the GROMACS 3.3 manual.
> > > > > There, dA/dl is calculated as
> > > > >
> > > > > dA/dl = SS{ (dH/dl) exp()dp dq } / SS{ exp()dp dq =
> <dA/dl>NVT;l
> > }
> > > > >
> > > > > where SS are doble integrals (sorry for the notation).
> > > > >
> > > > > My question is: how is (dH/dl) (in the middel-term of the
> > equation)
> > > > > calculated?
> > > > > My idea is that the difference V(L=1)-V(L=0) is calculated for
> > every
> > > > time
> > > > > step (irrespective of the lambda value of the simulation) and
> > <dG/dl>
> > > > is
> > > > > the time average of that difference.
> > > > >
> > > > > <dG/dl> = < V(L=1)(i)-V(L=0)(i)/1 >
> > > > >
> > > > > Is this correct?
> > > > >
> > > > >
> > > > > Thanks
> > > > >
> > > > >
> > >
> > >
> > >
> >
>
>
>
>
>
> ------------------------------
>
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>
> End of gmx-users Digest, Vol 31, Issue 23
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