[gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION
arun kumar
arunjones.kumar89 at gmail.com
Wed Nov 16 07:03:54 CET 2011
hi justin,
as u said i understand that there is inconsistency in the charges and
charge groups of PRODRG server itself.
can u suggest me any other softwares that i can rely on for this work.
Thanking you.
On Tue, Nov 15, 2011 at 7:48 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
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> 1. Re: ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION (Justin A. Lemkul)
> 2. RMSD (shahid nayeem)
> 3. Problem during GROMACS 4.5.5 installation (sai nitin)
> 4. Re: Problem during GROMACS 4.5.5 installation (Justin A. Lemkul)
> 5. Re: RMSD (Gianluca Santoni)
> 6. Re: RMSD (felmerino at uchile.cl)
> 7. Re: Positive potential energy for TFE solvent (Harpreet Basra)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 15 Nov 2011 06:40:31 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4EC24FAF.5050704 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> arun kumar wrote:
> > Dear friends,
> >
> > i had a problem while running the of protein-ligand complex simulation,
> > in which i have generated the ligand toplogy by using online Prodrg
> > server and iam using gromos 96.1froce field.
> >
> > there was an note and an error during minimization
> >
> > NOTE 2 [file trp.top]:
> > The largest charge group contains 15 atoms.
> > Since atoms only see each other when the centers of geometry of the
> charge
> > groups they belong to are within the cut-off distance, too large charge
> > groups can lead to serious cut-off artifacts.
> > For efficiency and accuracy, charge group should consist of a few
> atoms.
> > For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
> >
> > Analysing residue names:
> > There are: 223 Protein residues
> > There are: 1 Other residues
> > There are: 25853 Water residues
> > Analysing Protein...
> > Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> > into groups...
> > Number of degrees of freedom in T-Coupling group rest is 161838.00
> > Largest charge group radii for Van der Waals: 0.790, 0.356 nm
> > Largest charge group radii for Coulomb: 0.790, 0.399 nm
> >
> > WARNING 1 [file em.mdp]:
> > The sum of the two largest charge group radii (1.188798) is larger than
> > rlist (1.000000)
> >
> > i am using the mdp file the one that i copied from gromacs
> > protein-ligand tutorial
> >
> > can any one please explain these errors so that i can go farward in my
> work.
> >
>
>
> http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb
>
> > and i have a doubt, as there are other updated forcefields, how much
> > reliable is the gromos 96 ff....
> >
>
> The problem is not the reliability of Gromos96, but the reliability of
> PRODRG.
> Please read the paper linked from
> http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips to
> understand why
> you should almost certainly never use the charges and charge groups that
> PRODRG
> creates.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 15 Nov 2011 17:53:19 +0530
> From: shahid nayeem <msnayeem at gmail.com>
> Subject: [gmx-users] RMSD
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <CAB_3DJa8m-jooJb=CMSCMRds8jA-rzDM7GMDm+OKu7s7Qem8tA at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear all
> I am interested to get contour plot of residue RMSD vs time graph. I want
> to get the flexible and rigid regions of protein chain during simulation.
> g_rmsf does not gives me this plot.
> Please help
> shahid Nayeem
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> Message: 3
> Date: Tue, 15 Nov 2011 14:03:03 +0100
> From: sai nitin <sainitin7 at gmail.com>
> Subject: [gmx-users] Problem during GROMACS 4.5.5 installation
> To: gmx-users at gromacs.org
> Message-ID:
> <CAGJtc4NWdF9A2V9T8eep1JMa+s4KECOa6p8RNL6vNM_M7HQkAw at mail.gmail.com
> >
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>
> Hi all,
>
>
> I just started learning molecular dynamics analysis of protein-ligand
> complexes to do this i downloaded GROMACS 4.5.5 and tried to install
> according to Manual instructions executed following commands..
>
> ./configure
> make (when i executed this command it is showing following error *** No
> targets specified and no makefile found)
>
> Can any body help how to solved this...
>
> Thanks in advance
> --
>
> Sainitin D
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> ------------------------------
>
> Message: 4
> Date: Tue, 15 Nov 2011 08:13:40 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Problem during GROMACS 4.5.5 installation
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4EC26584.8060803 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> sai nitin wrote:
> > Hi all,
> >
> >
> > I just started learning molecular dynamics analysis of protein-ligand
> > complexes to do this i downloaded GROMACS 4.5.5 and tried to install
> > according to Manual instructions executed following commands..
> >
> > ./configure
> > make (when i executed this command it is showing following error *** No
> > targets specified and no makefile found)
> >
>
> Configuration failed. Simply specifying ./configure without any options is
> often insufficient. Please follow the installation guide online.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 15 Nov 2011 21:18:16 +0800
> From: Gianluca Santoni <gianluca.santoni at ibs.fr>
> Subject: Re: [gmx-users] RMSD
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4EC26698.7000804 at ibs.fr>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 11/15/11 8:23 PM, shahid nayeem wrote:
> > Dear all
> > I am interested to get contour plot of residue RMSD vs time graph. I
> > want to get the flexible and rigid regions of protein chain during
> > simulation. g_rmsf does not gives me this plot.
> > Please help
> > shahid Nayeem
> >
> >
> >
> Try g_rmsf -res , it could be useful, maybe.
>
> --
> Gianluca Santoni,
> Institut de Biologie Structurale
> 41 rue Horowitz
> Grenoble
> _________________________________________________________
> Please avoid sending me Word or PowerPoint attachments.
> See http://www.gnu.org/philosophy/no-word-attachments.html
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> Message: 6
> Date: Tue, 15 Nov 2011 10:32:16 -0300 (GMT-03:00)
> From: "felmerino at uchile.cl" <felmerino at uchile.cl>
> Subject: Re: [gmx-users] RMSD
> To: <gmx-users at gromacs.org>
> Message-ID:
> <10450993.2631321363936014.JavaMail.defaultUser at defaultHost>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> In any case, if you really want to see flexibility then you need RMSF and
> not RMSD as the later will only tell you about how similar is the
> configuration of a sidechain compared to a reference frame. If that is
> still what you want i think VMD has a tool for that in the timeline plugin.
>
>
>
> regards
>
>
>
> Felipe
> ----Mensaje original---- De: gianluca.santoni at ibs.fr Fecha: 15-nov-2011
> 10:18 Para: "Discussion list for GROMACS users"<gmx-users at gromacs.org>
> Asunto: Re: [gmx-users] RMSD On 11/15/11 8:23 PM, shahid nayeem wrote:
> Dear all
> I am interested to get contour plot of residue RMSD vs time graph.
> I want to get the flexible and rigid regions of protein chain
> during simulation. g_rmsf does not gives me this plot.
> Please help
> shahid Nayeem
>
>
> Try g_rmsf -res , it could be useful, maybe.
> --
> Gianluca Santoni,
> Institut de Biologie Structurale
> 41 rue Horowitz
> Grenoble
> _________________________________________________________
> Please avoid sending me Word or PowerPoint attachments.
> See http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
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> Message: 7
> Date: Tue, 15 Nov 2011 19:48:06 +0530
> From: Harpreet Basra <harpreetk.basra at gmail.com>
> Subject: [gmx-users] Re: Positive potential energy for TFE solvent
> To: gmx-users at gromacs.org
> Message-ID:
> <CAEAiM5sSFLvHhe+ZM1Z60T4b-BkuJ5VcPbEfza92g255qY27rA at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Mark,
>
> Thanks for the quick reply. But i have already done what u suggested.
>
>
> >
> > On 15/11/2011 6:06 PM, Harpreet Basra wrote:
> > > Hi
> > > I am still stuck with same problem of obtaining positive potential
> > > energy.
> > > >>On 11/11/2011 5:07 PM, Harpreet Basra wrote:
> > > >> Hi
> > > >>
> > > >> I am trying to generate an equilibrated box of 216 TFE molecules.To
> > > >> generate the 216 TFE molecule box i performed following steps:
> > > >
> > > >A suggested workflow can be found here
> > > >http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation
> > > I have been following this link only.
> > > >
> > > >
> > > >> 1) I got the tfe.gro file and created a cubic box of edge length =
> > > >> 0.516 nm containing 1 TFE molecule (at its center), using the
> > > >> following command:
> > > >>
> > > >>>> editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516
> > > >> I chose this length because in the tfe.gro file dimensions of the
> TFE
> > > >> molecule are 0.516 0.516 0.516.
> > > >
> > > >That's not a good reason. Choose a volume and shape that makes sense
> for
> > > >your target density. Cubic probably doesn't make sense when a
> > > >rectangular shape is possible. Then you'll probably want to choose
> -nbox
> > > >differently later.
> > > I chose a rectangular box too. still i get a positive value for PE and
> > > moreover all the molecules move towards two opposite walls of the box.
> > > I am not sure that the way I am using the genconf command is the
> > > correct way. because I have tried every other possibility for not
> > > getting a positive potential, with no success. So here are my .gro
> > > file and the topology file for TFE.
> > > *****tfe.gro file*****
> > > 7
> > >
> > > 1TFE F1T 1 0.444 0.344 0.246
> > >
> > > 1TFE CT 2 0.334 0.245 0.246
> > >
> > > 1TFE F2T 3 0.350 0.160 0.364
> > >
> > > 1TFE F3T 4 0.350 0.160 0.127
> > >
> > > 1TFE CH2T 5 0.187 0.326 0.246
> > >
> > > 1TFE OT 6 0.075 0.220 0.246
> > >
> > > 1TFE HT 7 -0.019 0.266 0.246
> > >
> > > 0.49174 0.49174 0.49174
> > >
> > > ****topology file****
> > >
> > > [ moleculetype ]
> > >
> > > ; Name nrexcl
> > >
> > > TFE 3
> > >
> > > [ atoms ]
> > >
> > > ; nr type resnr resid atom cgnr charge mass
> > >
> > > 1 FTFE 1 TFE F1T 1 -0.170 18.9984
> > >
> > > 2 CTFE 1 TFE CT 1 0.452 12.0110
> > >
> > > 3 FTFE 1 TFE F2T 1 -0.170 18.9984
> > >
> > > 4 FTFE 1 TFE F3T 1 -0.170 18.9984
> > >
> > > 5 CHTFE 1 TFE CH2T 1 0.273 14.0270
> > >
> > > 6 OTFE 1 TFE OT 1 -0.625 15.9994
> > >
> > > 7 H 1 TFE HT 1 0.410 1.0080
> > >
> > > [ bonds ]
> > >
> > > ; ai aj fu c0, c1, ...
> > >
> > > 2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1
> > >
> > > 2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2
> > >
> > > 2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3
> > >
> > > 2 5 2 0.153 7150000.0 0.153 7150000.0 ; C1 C2
> > >
> > > 5 6 2 0.143 8180000.0 0.143 8180000.0 ; C2 O
> > >
> > > 6 7 2 0.100 15700000.0 0.100 15700000.0 ; O H
> > >
> > > [ pairs ]
> > >
> > > ; ai aj fu c0, c1, ...
> > >
> > > 1 6 1 ; F1 O
> > >
> > > 2 7 1 ; C1 H
> > >
> > > 3 6 1 ; F2 O
> > >
> > > 4 6 1 ; F3 O
> > >
> > > [ angles ]
> > >
> > > ; ai aj ak fu c0, c1, ...
> > >
> > > 1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2
> > >
> > > 1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3
> > >
> > > 1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2
> > >
> > > 3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3
> > >
> > > 3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2
> > >
> > > 4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2
> > >
> > > 2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O
> > >
> > > 5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H
> > >
> > > [ dihedrals ]
> > >
> > > ; ai aj ak al fu c0, c1, m, ...
> > >
> > > 6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1
> > >
> > > 2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H
> > >
> > > and to construct a box of TFE solvent i took the tfe.gro file and
> > > replicated the TFE molecule by using
> > > genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6
> > > can u plz suggest is it that I am using genconf in a wrong way that it
> > > is causing this problem? I am not sure how many molecules (-nbox
> > > option in genconf) should i keep in the box in order to get a mass
> > > density of 1383g/L for TFE.
> >
> > That link says "Work out how much volume a single molecule would have in
> > the box of your chosen density and size. Useeditconf
> > <http://www.gromacs.org/editconf>to place a box of that size around your
> > single molecule." It does not seem to me that you have done this.
> >
> > Mark
> >
>
> I did place the *single molecule* in a box of size required to get a
> density of 1383 g/L. I also checked the density of the solvent box
> (containing 216 molecules after NVT equilibration for 200 ps) I constructed
> the average value comes out to be 1397 g/L with a std deviation of 30 g/L,
> thus it seems range. Moreover, the potential energy of this one molecule
> (tfe.gro) was coming out to be highly negative (-6.4E+08 kJ/mol). But on
> generating a solvent system with 216 TFE molecules the energy becomes
> (1.9E+04 kJ/mol).
>
> Harpreet
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--
Arun Kumar Somavarapu
Project-JRF
Dr. Prasanna's lab
TMC, ACTREC
Navi Mumbai-410210
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