[gmx-users] gromacs.org_gmx-users Digest, Vol 175, Issue 40
Rahma Dahmani
rahma.dahmani at fst.utm.tn
Tue Nov 13 08:05:30 CET 2018
Hi Justin,
Thanks for your response,
I am using a topology file constructed from amber tools ...
Le mar. 13 nov. 2018 à 01:04, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> a écrit :
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> Today's Topics:
>
> 1. Re: Expansion system after NVT Equilibrium in Gromacs
> (Justin Lemkul)
> 2. Re: Input file for energy minimization for solvated system:
> Error (Justin Lemkul)
> 3. Re: pdb2gmx fatal error (Ali Khodayari)
> 4. Re: Group WAT referenced in the .mdp file was not found in
> the index file (Justin Lemkul)
> 5. Re: atomtype OV not found (Justin Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 12 Nov 2018 18:59:01 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Expansion system after NVT Equilibrium in
> Gromacs
> Message-ID: <f2bfba5b-cc1a-329b-de4b-5b264d4e489f at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/11/18 12:16 PM, yasminesophi at students.itb.ac.id wrote:
> > i'm currently running a simulation protein in water using gromacs with
> force field gromos96 54a7. the protein structure that i used is from
> modeller. there is no problem untill the minimization step but the system
> is expanding after NVT equilibration. and when i try to do NPT
> equilibration after that, the system is shrinking [the box volume is
> smaller than before]
> >
> > i'm using the parameter from gromacs tutorial "lysozyme in water" with
> hbonds constraints for NVT equilibration and the temperature is 298 K.
> please help me to solve this problem
>
> Don't use input files from my tutorial if you're using GROMOS. The
> nonbonded settings and required constraints are different, as hopefully
> I make very clear...
>
> In any case, if you're running NPT, naturally the system will expand and
> contract. There's no reason that it won't, as that is precisely what a
> barostat does. If your system is changing, that just means your initial
> conditions are not compatible with the specified NPT ensemble and the
> properties of the system have to adjust.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 12 Nov 2018 19:00:23 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Input file for energy minimization for
> solvated system: Error
> Message-ID: <ab0c1a33-c48d-9cdc-c4db-1105821982d5 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/11/18 3:04 PM, Neena Susan Eappen wrote:
> > Hello GROMACS users,
> >
> >
> > I was trying to create an input file for energy minimization of solvated
> system, using the following command:
> >
> > grompp -v -f minim.mdp -c protein-solvated.gro -p protein.top -o
> protein-EM-solvated.tpr
> >
> > Got the following error:
> > number of coordinates in coordinate file (1y6l-solvated.gro, 181577)
> does not match topology (1y6l.top, 182265).
> >
> > I think the following error occurred because I skipped the following
> step:
> > Edit the topology file and decrease the number of solvent molecules.
> Also add a line specifying the number of NA ions and a line specifying the
> amount of CL.
> >
> > My question:
> >
> > 1. How to open the topology file?
>
> A topology is a plain text file. Use a plain-text editor.
>
> > 2. How do I determine number of NA and CL ions added? I just saw a
> massive list of these counterions being added, but not the total number.
>
> genion tells you this.
>
> > 3. My net charge on the protein was 6+, why do I need to add Na+
> ions?
>
> We don't know what your genion command was, so we can't say.
>
> Let solvate and genion do the work for you. Use the -p flag to have
> those programs update your topology for you, especially if you are not
> familiar with their contents or how to edit them. See e.g.
> http://www.mdtutorials.com/gmx/lysozyme/index.html
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 13 Nov 2018 00:01:24 +0000
> From: Ali Khodayari <ali.khodayari at student.kuleuven.be>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] pdb2gmx fatal error
> Message-ID: <D295CEF0-7278-4486-93F3-0D3847350005 at student.kuleuven.be>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Justin,
>
> Thank you for your full explanation. That made it all clear now.
>
> Kind regards,
> Ali
>
> > On 13 Nov 2018, at 00:57, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >
> >
> > On 11/8/18 1:37 PM, Ali Khodayari wrote:
> >> Dear Justin,
> >>
> >> Thank you for your response. Yet, I have not been able to solve the
> problem.
> >>
> >> The structure looks fine but gromacs is complaining about a dangling
> atom at
> >> one of the terminal ends, if I choose no terminal to be added. While,
> >
> > You can't "see" a dangling bond by visualizing the structure. That term
> refers exclusively to an incomplete terminus in terms of the *topology*
> that is being generated for the system. Maybe atoms are missing or an
> inappropriate terminal patch is being applied; either would generate that
> error. But again I emphasize the fact that a chain of glucose has first and
> last residues that are structurally and topologically different from
> internal, linked monomers. It's basic chemistry.
> >
> > <snip>
> >
> >> ATOM 27 O3 GLC0 2 3.909 5.661 5.002 1.00 0.04
> >> O
> >> ATOM 28 HO4 GLC0 2 4.850 3.729 10.263 1.00 0.00
> >> H
> >> ATOM 29 O1 GLC0 1 3.396 2.685 4.467 1.00 0.04
> >> O
> >
> > Here's your problem - your residue numbers alternate back and forth
> between 1 and 2. pdb2gmx ignores these and uses its own numbering,
> incrementing the internal counter whenever the residue number changes. So
> to pdb2gmx, your input file is full of incomplete residues.
> >
> >> ATOM 30 O5 GLC0 2 4.225 2.770 8.173 1.00 0.04
> >> O
> >> ATOM 31 O6 GLC0 2 3.558 0.309 5.328 1.00 0.04
> >> O
> >> ATOM 32 H1 GLC0 2 2.572 4.115 8.609 1.00 0.00
> >> H
> >> ATOM 33 H2 GLC0 2 5.244 5.151 7.307 1.00 0.00
> >> H
> >> ATOM 34 H3 GLC0 2 2.361 4.651 6.153 1.00 0.00
> >> H
> >> ATOM 35 H4 GLC0 2 5.141 3.258 5.636 1.00 0.00
> >> H
> >> ATOM 36 H5 GLC0 2 2.480 2.262 6.979 1.00 0.00
> >> H
> >> ATOM 37 H61 GLC0 2 3.879 0.196 7.468 1.00 0.00
> >> H
> >> ATOM 38 H62 GLC0 2 5.286 0.920 6.494 1.00 0.00
> >> H
> >> ATOM 39 HO2 GLC0 2 2.496 6.480 7.836 1.00 0.00
> >> H
> >> ATOM 40 HO3 GLC0 2 5.015 5.674 4.919 1.00 0.00
> >> H
> >> ATOM 41 HO6 GLC0 2 2.453 0.270 5.418 1.00 0.00
> >> H
> >> ATOM 42 O3 GLC0 1 3.852 1.653 -0.348 1.00 0.00
> >> O
> >
> > As above, now you're again going back and forth between 1 and 2, so
> pdb2gmx sees a new residue, which is not correct.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
> > --
> > 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.
>
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 12 Nov 2018 19:01:29 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Group WAT referenced in the .mdp file was not
> found in the index file
> Message-ID: <b6d71208-268a-dbc6-0a7b-3c015dec1b7b at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/12/18 7:14 AM, Rahma Dahmani wrote:
> > Hi GMX users,
> >
> > i double checked in my topology and gro files that i am using the same
> > moleculetype ( LIG and WAT) but when i run grompp for T equilibration i
> get
> > an error message """" Group WAT referenced in the .mdp file was not found
> > in the index file """"
> > PS: i am not using an index file and i modified tc-grps, in nvt.mdp
> file ,
> > to :
> > tc-grps = LIG WAT .
> >
>
> The error means that "WAT" is not a valid group. What is it in your
> topology? The default water [moleculetype] in all GROMACS topologies is
> "SOL," not "WAT."
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 12 Nov 2018 19:02:52 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] atomtype OV not found
> Message-ID: <10e914b3-e342-78e3-141e-7a541cc18cff at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/12/18 8:41 AM, Farial Tavakoli wrote:
> > Dear Mark
> >
> > I changed the way of topology generating in AMBER. The peptidic ligand
> (has
> > 2 phosphotyrosine residues) topology was generated using amber. all of
> the
> > files that I have in my working directory are, Leaprc.ff99SB,
> > Learc.phosaa10, frcmod.phosaa10, ligand.inpcrd, ligand.prmtop. The
> only
> > thing that I know to convert amber format to gromacs format is to use
> > acpype python script :
> > python acpype -p ligand.prmtop -x ligand.inpcrd
> > The .gro and .top files were generated. protein topology was generated
> > using amber99SB ff in gromacs and then complex.gro and .top files were
> > modified according to the tutorial in gromacs. But now, when I issue this
> > command:
> > gmx grompp -f .mdp -c .gro -p .top -o ions.tpr
> > I face to this error:
> > ERROR 1 [file mig_GMX.itp, line 60]:
> > Atomtype OV not found
> > OV atom is related to leaprc.phosaa10 file and I dont know what should I
> do
> > now?
> > I think , the leaprc.phosaa10 file has to be added to aminoacid.rtp file
> of
> > amber99SB.ff but I dont know how to convert it to gromacs format file?
> > Am I right?
> > WOuld you please guide me how to remove this Error?
>
> Your force field has to account for all the atom types required to run
> the simulation. You don't need to modify any .rtp files if you've
> already got a topology produced by other means. But that topology should
> be edited to introduce any new atom types required, associated bonded
> parameters, etc. When you do nonstandard things, you have to take
> nonstandard approaches...
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> End of gromacs.org_gmx-users Digest, Vol 175, Issue 40
> ******************************************************
>
--
*Rahma Dahmani Doctorante en CHIMIE Unité de Recherche: Physico-Chimie des
Matériaux à l'état condensé, Laboratoire de Chimie Théorique et
Spectroscopie MoléculaireUniversité de Tunis El Manar, Faculté des Sciences
de Tunis Campus Universitaire Farhat Hached - BP n ° 94 - Rommana 1068,
Tunisie Tél: (+216) 28151042*
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