[gmx-users] -vsite hydrogen
Wojciech Kopeć
9000nin at gmail.com
Mon Dec 29 21:04:08 CET 2014
We have tested virtual sites with CHARMM36 lipids; straightforward usage
gives too ordered membranes. We have created custom virtual sites
construction for lipid hydrogens and used them for pure membranes as well
as for membrane proteins, and the differences between membrane properties
with virtual sites and without are usually minor (but still noticeable).
The parameters can be found here http://memphys.dk/node/71 and the paper
http://pubs.acs.org/doi/abs/10.1021/ct500100f
Wojciech
Message: 1
Date: Mon, 29 Dec 2014 10:27:47 -0500
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] -vsite hydrogen
Message-ID: <54A172F3.5040700 at vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 12/29/14 6:28 AM, h.alizadeh at znu.ac.ir wrote:
> Dear Users,
> I am simulating a membrane protein with charmm ff with a 2fs time step.
> How the results will be affected if I use a 5fs time step by using "-vsite
> hydrogen" option in pdb2gmx? Do my results loose their accuracy if I use
> this option?
Well, it's easy to test. The membrane properties that are expected to be
observed are very easy to quantify. We didn't test our CHARMM36 port with
virtual sites at all, so we cannot recommend such usage. Test thoroughly
before
doing any real production work. Membranes are extremely sensitive to
alteration.
-Justin
On Mon, Dec 29, 2014 at 8:52 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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> Today's Topics:
>
> 1. Re: -vsite hydrogen (Justin Lemkul)
> 2. Re: Obtaining PMF for change in domain position (Justin Lemkul)
> 3. pdb information (elham tazikeh)
> 4. Re: pdb information (Justin Lemkul)
> 5. Re: Obtaining PMF for change in domain position (Abhi Acharya)
> 6. Gromacs error regarding default gromos bond type and angle
> type (Negar Parvizi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 29 Dec 2014 10:27:47 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] -vsite hydrogen
> Message-ID: <54A172F3.5040700 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/29/14 6:28 AM, h.alizadeh at znu.ac.ir wrote:
> > Dear Users,
> > I am simulating a membrane protein with charmm ff with a 2fs time step.
> > How the results will be affected if I use a 5fs time step by using
> "-vsite
> > hydrogen" option in pdb2gmx? Do my results loose their accuracy if I use
> > this option?
>
> Well, it's easy to test. The membrane properties that are expected to be
> observed are very easy to quantify. We didn't test our CHARMM36 port with
> virtual sites at all, so we cannot recommend such usage. Test thoroughly
> before
> doing any real production work. Membranes are extremely sensitive to
> alteration.
>
> -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: 2
> Date: Mon, 29 Dec 2014 10:29:18 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Obtaining PMF for change in domain position
> Message-ID: <54A1734E.5000206 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/29/14 6:57 AM, Abhi Acharya wrote:
> > Hello GROMACS Users,
> >
> > This is a problem I am facing for the first time. Kindly guide be to the
> > best options.
> >
> > I have a protein which has two large domains connected by a flexible
> linker
> > peptide (~10 aa). The two domains seem to interact with each other and
> have
> > been crystallized in three different conformations. I want to calculate
> the
> > change in binding energy of the two domains wrt change in their relative
> > position, i.e. keeping position of one domain constant what is change in
> > binding energy as the other domain moves from conformation 1, through
> > conformation 2 to finally, conformation 3. What is the best way to do so?
> >
>
> You need to describe what these three conformations are. Do they involve
> rotations of the domains with respect to one another, or is it a simple
> linear
> distance that varies?
>
> > At first, I considered using umbrella sampling to address the problem.
> Here
> > too, I was not sure how to write a pull code for such a complex reaction
> > coordinate. Also, even if I can generate the conformations, what would be
> > the ideal number of windows that would be needed to correctly generate a
> > PMF ? My feeling is it would be a large number, but again it just a
> guess.
> > Is there is a better way than this?
> >
>
> Hard to know a priori. You may need some trial and error here, but with
> umbrella sampling it's trivial to just go back and add windows, since the
> simulations are still all independent of one another.
>
> -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: 3
> Date: Mon, 29 Dec 2014 19:38:13 +0330
> From: elham tazikeh <elham.tazikeh at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] pdb information
> Message-ID:
> <CAEg2dSZWt6eSRFvRUE7SJc_GzY=
> LcrndRXbTYeDitDJfM9p53Q at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear GMX users
> i d like to know about pdb information
> for instance, when i defined concentration of an ion by genion (-conc),
> gromacs added ion(s) to my structure
>
> Now, my question is:
> in a pdb e.g. (1ZE9: Amyloid beta peptide+Zn+2), there is only one cation
> in pdb file
> i want to know about its concentration?
> my mean is one Zn+2 ion equal *what concentration*?
> regards
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 29 Dec 2014 11:12:20 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] pdb information
> Message-ID: <54A17D64.5030604 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/29/14 11:08 AM, elham tazikeh wrote:
> > Dear GMX users
> > i d like to know about pdb information
> > for instance, when i defined concentration of an ion by genion (-conc),
> > gromacs added ion(s) to my structure
> >
> > Now, my question is:
> > in a pdb e.g. (1ZE9: Amyloid beta peptide+Zn+2), there is only one cation
> > in pdb file
> > i want to know about its concentration?
> > my mean is one Zn+2 ion equal *what concentration*?
> > regards
> >
>
> Think back to general chemistry. Without a defined volume, you can't
> define
> concentration...
>
> -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: Mon, 29 Dec 2014 22:04:56 +0530
> From: Abhi Acharya <abhi117acharya at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Obtaining PMF for change in domain position
> Message-ID:
> <
> CAB1aw3x8qFnnK098NVYoXnDCxqftyEnxKPDis2MSOi2dj+cjnw at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> On Mon, Dec 29, 2014 at 8:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 12/29/14 6:57 AM, Abhi Acharya wrote:
> >
> >> Hello GROMACS Users,
> >>
> >> This is a problem I am facing for the first time. Kindly guide be to the
> >> best options.
> >>
> >> I have a protein which has two large domains connected by a flexible
> >> linker
> >> peptide (~10 aa). The two domains seem to interact with each other and
> >> have
> >> been crystallized in three different conformations. I want to calculate
> >> the
> >> change in binding energy of the two domains wrt change in their relative
> >> position, i.e. keeping position of one domain constant what is change in
> >> binding energy as the other domain moves from conformation 1, through
> >> conformation 2 to finally, conformation 3. What is the best way to do
> so?
> >>
> >>
> > You need to describe what these three conformations are. Do they involve
> > rotations of the domains with respect to one another, or is it a simple
> > linear distance that varies?
>
>
> Yes, there are significant rotations+translations along different axes
> involved which makes it challenging. Is there a way to model such movements
> using the pull code?
>
> >
> > At first, I considered using umbrella sampling to address the problem.
> Here
> >> too, I was not sure how to write a pull code for such a complex reaction
> >> coordinate. Also, even if I can generate the conformations, what would
> be
> >> the ideal number of windows that would be needed to correctly generate a
> >> PMF ? My feeling is it would be a large number, but again it just a
> guess.
> >> Is there is a better way than this?
> >>
> >>
> > Hard to know a priori. You may need some trial and error here, but with
> > umbrella sampling it's trivial to just go back and add windows, since the
> > simulations are still all independent of one another.
> >
>
> My concern is that since the domain movement from initial to final
> conformation is of about 10 nm, the number of windows required maybe too
> large. I read that the windows need to be spaced close enough so that each
> one samples some part of the next window. My system is also very large
> (200K atoms), so it seems to be computationally very expensive.
>
> I was just now thinking to reduce the problem to conducting umbrella
> sampling for each conformation, simply using COM distance of the two
> domains as the reaction coordinate to obtain the PMF in each case. From the
> PMF, the binding energy of the domains in each conformation can be obtain.
> This will allow me to circumvent the complications introduced by domain
> rotations and maybe reduce the number of simulations required a bit . Will
> this be a correct approach?
>
> Thank you.
>
> Abhishek Acharya
>
> >
> > -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.
> >
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 29 Dec 2014 19:48:49 +0000 (UTC)
> From: Negar Parvizi <negar.parvizi at yahoo.com>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: [gmx-users] Gromacs error regarding default gromos bond type
> and angle type
> Message-ID:
> <
> 1388645856.2400116.1419882529365.JavaMail.yahoo at jws106150.mail.bf1.yahoo.com
> >
>
> Content-Type: text/plain; charset=UTF-8
>
>
>
>
> Dear Gromacs users
> we want to simulate 1EA1 pdf file using gromacs. (according to justin
> tutorial).
>
> This pdf file contains two cofactors including TPF and HEM. Our next step
> is to dock some antifungal drugs to this protein which is cytochrome of the
> fungi.
> As the TPF was not located in the active site and due to the lack of
> topology informtaion for this cofactor in gromos force fields, we omitted
> the TPF .
> Then we performed pdb2gmx on the protein along with the HEM cofactor. The
> pdb2gmx did not give error, so we were satisfied with the topology file.
>
> But when in the step of adding ions, we performed grommp command to get
> the ions.tpr file, we faced with 7 errors:
>
> these errors were saying that there are not gromos default bond type or
> angle type or dihedral type for specified lines in the topology file.
>
> I checked the atom numbers that were present in those bonds, angles and
> dihedrals and came to the conclusion hat all of them contain (Fe) atom
> which is present in the HEM cofactor.
>
> It seems that pdb2gmx command is not able to specify gromos default bond
> type or angle type whenever Fe is there.
>
> Now please guide us to solve the problem.
> what should I put in the vacancy spaces for these bond type or angle
> types. I mean what (gb_? or ga_?)
> and why the pdb2gmx did not gave error???
>
> Thanks alot
>
>
>
> --
> Dr. Delara Mohammad-Aghaie
> Assistant Professor of Physical Chemistry
> Department of Chemistry
> Shiraz University of Technology
> Shiraz
> Iran
>
>
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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