[gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION
sai nitin
sainitin7 at gmail.com
Wed Nov 16 10:07:59 CET 2011
Hi,
You can try swissparam online tool to generate protein and ligand
topologies..
Cheers,
Nitin
On Wed, Nov 16, 2011 at 7:03 AM, arun kumar <arunjones.kumar89 at gmail.com>wrote:
> 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:
>>
>> 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>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> 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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--
Sainitin D
PhD student
Bioinformatics Group
Biotechnology Center
Technische Universität Dresden
Tatzberg 47/49
01307 Dresden, Germany
Tel Lab:+49 (0)351 463 40060
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