[gmx-users] gromacs.org_gmx-users Digest, Vol 137, Issue 154
Raag Saluja
saluja.raag at gmail.com
Wed Sep 30 15:11:44 CEST 2015
thank you so much, Dr. Repic!
On Wed, Sep 30, 2015 at 5:55 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: mutating the protein (Repic Matej)
> 2. bond, angles and dihedrals in the topology file
> (faride badalkhani)
> 3. Re: mutating the protein (Catarina A. Carvalheda dos Santos)
> 4. Re: bond, angles and dihedrals in the topology file
> (Justin Lemkul)
> 5. Re: Free energy in octanol and water (Justin Lemkul)
> 6. Re: bond, angles and dihedrals in the topology file
> (faride badalkhani)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 30 Sep 2015 11:19:17 +0000
> From: Repic Matej <matej.repic at epfl.ch>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] mutating the protein
> Message-ID: <D2318FD2.12845%matej.repic at epfl.ch>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I do not think this is something gromacs supports, but you can use several
> other programs like VMD, Chimera, Modeler etc, depending on the method of
> mutating a residue. I usually use chimera on macosx or linux like this:
>
> echo "open protein.pdb; swapaa leu :333.a; write 0 333leu.pdb" | chimera
> --nogui
>
> This command opens the protein.pdb, swaps the amino acid 333 on chain a,
> and saves the pdb as 333leu.pdb.
>
> Best,
>
>
> ------------------------------------------------------
> Dr. Matej Repic
> Ecole Polytechnique F?d?rale de Lausanne
> Laboratory of Computational Chemistry and Biochemistry
> SB - ISIC ? LCBC
> BCH 4108
> CH - 1015 Lausanne
> ------------------------------------------------------
>
>
>
>
>
>
>
> On 9/30/15, 11:55, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
> behalf of Raag Saluja" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> on behalf of saluja.raag at gmail.com> wrote:
>
> >Hi!
> >
> >Gromacs is a beautiful software! I have been able to understand the
> >dynamics of this protein I was trying to study.
> >
> >I wanted to see how the various amino acids could affect its dynamics. So
> >I
> >wanted to mutate the protein by replacing one particular amino acid by
> >another one. How may I do that?
> >
> >Thank you in advance!
> >
> >--
> >Regards,
> >Raag
> >--
> >Gromacs Users mailing list
> >
> >* Please search the archive at
> >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >posting!
> >
> >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> >* For (un)subscribe requests visit
> >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >send a mail to gmx-users-request at gromacs.org.
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 30 Sep 2015 14:51:39 +0330
> From: faride badalkhani <farideh.khamseh at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] bond, angles and dihedrals in the topology file
> Message-ID:
> <
> CA+G_2tfGxPSof-bRXV6hOt2gzSKnVJNrKvif8+j_TavPeiEFbw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear all,
>
> Could you tell me what is wrong when there are some strange bond, angles
> and dihedrals in the topology file after executing pdb2gmx command?
> for example atoms 1 and 27 do not have any connectivity, but pdb2gmx
> generate them as [bonds]. A similar problem occurs in case of angles and
> dihedrals.
>
> Truly yours,
> Farideh
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 30 Sep 2015 12:32:43 +0100
> From: "Catarina A. Carvalheda dos Santos"
> <c.a.c.dossantos at dundee.ac.uk>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] mutating the protein
> Message-ID:
> <CAGo0FV9bdoT2TxuAY4BZa3F4Z1oqAs34sEEW32oFm=oFH=
> JeFg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi there,
>
> I don't know about other options, but PyMOL allows you to do this using the
> "Mutagenesis Wizard" (just google it and you'll find step-by-step
> instructions in the PyMOL Wiki).
> Whatever you use, make sure that you select a proper side chain orientation
> (rotamer) when performing the mutation. This will avoid clashes between
> protein atoms and therefore problems during the energy minimization step.
>
> Regards,
>
>
>
>
> On 30 September 2015 at 12:19, Repic Matej <matej.repic at epfl.ch> wrote:
>
> > I do not think this is something gromacs supports, but you can use
> several
> > other programs like VMD, Chimera, Modeler etc, depending on the method of
> > mutating a residue. I usually use chimera on macosx or linux like this:
> >
> > echo "open protein.pdb; swapaa leu :333.a; write 0 333leu.pdb" | chimera
> > --nogui
> >
> > This command opens the protein.pdb, swaps the amino acid 333 on chain a,
> > and saves the pdb as 333leu.pdb.
> >
> > Best,
> >
> >
> > ------------------------------------------------------
> > Dr. Matej Repic
> > Ecole Polytechnique F?d?rale de Lausanne
> > Laboratory of Computational Chemistry and Biochemistry
> > SB - ISIC ? LCBC
> > BCH 4108
> > CH - 1015 Lausanne
> > ------------------------------------------------------
> >
> >
> >
> >
> >
> >
> >
> > On 9/30/15, 11:55, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
> > behalf of Raag Saluja" <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> > on behalf of saluja.raag at gmail.com> wrote:
> >
> > >Hi!
> > >
> > >Gromacs is a beautiful software! I have been able to understand the
> > >dynamics of this protein I was trying to study.
> > >
> > >I wanted to see how the various amino acids could affect its dynamics.
> So
> > >I
> > >wanted to mutate the protein by replacing one particular amino acid by
> > >another one. How may I do that?
> > >
> > >Thank you in advance!
> > >
> > >--
> > >Regards,
> > >Raag
> > >--
> > >Gromacs Users mailing list
> > >
> > >* Please search the archive at
> > >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >posting!
> > >
> > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > >* For (un)subscribe requests visit
> > >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > >send a mail to gmx-users-request at gromacs.org.
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> > The University of Dundee is a registered Scottish Charity, No: SC015096
> >
>
>
>
> --
> Catarina A. Carvalheda
>
> PhD Student
> Computational Biology Division
> School of Life Sciences
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 30 Sep 2015 07:33:19 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] bond, angles and dihedrals in the topology
> file
> Message-ID: <560BC87F.2060908 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 9/30/15 7:21 AM, faride badalkhani wrote:
> > Dear all,
> >
> > Could you tell me what is wrong when there are some strange bond, angles
> > and dihedrals in the topology file after executing pdb2gmx command?
> > for example atoms 1 and 27 do not have any connectivity, but pdb2gmx
> > generate them as [bonds]. A similar problem occurs in case of angles and
> > dihedrals.
> >
>
> Impossible to say without knowing what you're actually doing. Please
> always
> provide a full description of your system, your pdb2gmx command, and any
> relevant output, snippets of files, etc.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 30 Sep 2015 07:33:31 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Free energy in octanol and water
> Message-ID: <560BC88B.80708 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 9/30/15 3:13 AM, Gmx QA wrote:
> > Hi Justin
> >
> > Thanks, that is a good suggestion, I will try that.
> > Besides running multiple replicates, is there something else that is
> > obviously wrong with my method?
> >
>
> Not that I can see.
>
> -Justin
>
> > Best
> > /PK
> >
> >
> >
> >
> > 2015-09-29 19:09 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
> >
> >>
> >>
> >> On 9/29/15 4:51 AM, Gmx QA wrote:
> >>
> >>> Hi gmx-users
> >>>
> >>> I am trying to calculate the free energy of solvation for a
> drug-molecule
> >>> in octanol and water.
> >>>
> >>> I am comparing two situations:
> >>>
> >>> A: Two systems, one with the drug in water only, and one with the drug
> in
> >>> pure octanol.
> >>>
> >>> B: drug in water only (same as in A), and then one box where I have
> added
> >>> 20% water to my octanol system (since mixtures of octanol and water
> >>> typically contains some water in the octanol phase).
> >>>
> >>> Then I run a series of free energy calculations per Justin's tutorial,
> 48
> >>> lambda points in total.
> >>> For system A I get a Delta-G for pure water of 39.07 kJ/mol, and 92.81
> >>> kJ/mol in pure octanol.
> >>>
> >>> For system B, the Delta-G for pure water is the same, but for the
> >>> octanol-box with 20% water the Delta-G is 95.99 kJ/mol.
> >>>
> >>> All of these results are obtained using gmx bar in gromacs 5.0.4.
> >>>
> >>> My main concern is that the Delta-G is higher in the water/octanol
> mixture
> >>> than in pure octanol, but I would have expected the reverse to be the
> >>> case?
> >>>
> >>>
> >> From experience, I can tell you it is very hard to get good
> convergence on
> >> such mixtures. You'll note that in npt.gro you effectively have two
> bands
> >> of water formed in the box, neither or which is particularly close to
> the
> >> API molecule. You'll probably get some microscopic phase separation.
> The
> >> route I've gone in the past is to generate several starting
> configurations
> >> (different random seeds when inserting the water molecules) and
> averaging
> >> over multiple runs. You should also do some error analysis of your
> results
> >> (both block averaging for convergence, and to compare the two DG values
> >> between the systems). Without error bars, you have no idea if those two
> >> values are at all meaningfully different.
> >>
> >> -Justin
> >>
> >> Is there something wrong with my protocol? The forcefield is
> >>> GAFF/amber99sb,and all production runs are 10 ns in length.
> >>>
> >>> Best
> >>> /PK
> >>>
> >>> I have uploaded copies of all input-files here:
> >>>
> >>> https://dl.dropboxusercontent.com/u/66785227/md.mdp
> >>> https://dl.dropboxusercontent.com/u/66785227/npt.gro
> >>> https://dl.dropboxusercontent.com/u/66785227/octanol_GMX.itp
> >>> https://dl.dropboxusercontent.com/u/66785227/API_gmx.itp
> >>> https://dl.dropboxusercontent.com/u/66785227/topol.top
> >>>
> >>>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==================================================
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 30 Sep 2015 15:54:57 +0330
> From: faride badalkhani <farideh.khamseh at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] bond, angles and dihedrals in the topology
> file
> Message-ID:
> <
> CA+G_2tf88+pOzPRVCwDwWEXW3kfgZakgOLGaeCTp3hkzpZq1bg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> I want to simulate a dendrimer (a hyperbranched polymer) in water. I have
> used the GROMOS 53A6 force field parameters, and I have done the following
> steps:
> 1- Defining new atom types that were not exist in .atp file.
> 2- Adding appropriate bonds, angles, dihedrals, and impropers into the
> ffbonded.itp file.
> 3- Defining nonbonded parameters in ffnonbonded.itp file according to
> GROMOS FF parameters.
> 4- Introducing residue building blocks along with [bonds], [angles],
> [impropers], and [dihedrals] in .rtp file.
>
> After using pdb2gmx I receive this command:
>
> You have successfully generated a topology from: g3n.pdb
> The CA force field and the spce water model are used.
>
> Then I define box and solvent without any problems, but there are many
> errors when I execute grompp command as follows:
> Error 892 [file topol.top, line 6147]
> No default G96Angle types
>
> and
> Error 904 [file topol.top, line 6159]
> No default Proper Dih. types
>
> However, when I checked these lines I understood that
> 1- many of these bonds, angles, and dihedrals are related to atoms that are
> not connected to each other, or
> 2- I have defined the appropriate bond, angle, or dihedral, but I do not
> know why pdb2gmx didn't assign them.
>
> you can see all the files via
> https://www.dropbox.com/s/c8csnchfdahe016/4MEHR.zip?dl=0
>
> Excuse me for my poor English,
>
> Truly yours,
> Farideh
>
> On Wed, Sep 30, 2015 at 3:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 9/30/15 7:21 AM, faride badalkhani wrote:
> >
> >> Dear all,
> >>
> >> Could you tell me what is wrong when there are some strange bond, angles
> >> and dihedrals in the topology file after executing pdb2gmx command?
> >> for example atoms 1 and 27 do not have any connectivity, but pdb2gmx
> >> generate them as [bonds]. A similar problem occurs in case of angles and
> >> dihedrals.
> >>
> >>
> > Impossible to say without knowing what you're actually doing. Please
> > always provide a full description of your system, your pdb2gmx command,
> and
> > any relevant output, snippets of files, etc.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
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> send a mail to gmx-users-request at gromacs.org.
>
> End of gromacs.org_gmx-users Digest, Vol 137, Issue 154
> *******************************************************
>
--
Regards,
Raag
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