[gmx-users] the solvent group SOL is not continuous
Justin A. Lemkul
jalemkul at vt.edu
Wed Jan 27 00:01:18 CET 2010
Miguel Quiliano Meza wrote:
> Hi , Justin.
>
> well.. I keep three water molecules from original PDB , my actual model
> was obtained by homology.
>
> my file *top shows this.
>
> [ molecules ]
> ; Compound #mols
> Protein 1 ----------> Also, Zn+2 is here
> SOL 3 --------> from template
> LIG 1
> SOL 91231------->added with genbox
>
> Now, in my *pdb file obtained with genbox there are no blocks,
>
> ...............
> ...........................
> ATOM 1721 O1 SER 185 78.315 86.779 66.412 1.00 0.00
> ATOM 1722 O2 SER 185 78.467 89.180 66.704 1.00 0.00
> ATOM 1723 Zn ZN 186 70.487 59.483 68.899 1.00 0.00
> ATOM 1724 OW HOH 187 69.331 58.199 67.904 1.00 0.00
> ATOM 1725 HW1 HOH 187 70.147 58.199 68.481 1.00 0.00
> ATOM 1726 HW2 HOH 187 68.515 58.199 68.481 1.00 0.00
> ATOM 1727 OW HOH 188 70.810 60.669 67.316 1.00 0.00
> ATOM 1728 HW1 HOH 188 71.626 60.669 67.893 1.00 0.00
> ATOM 1729 HW2 HOH 188 70.810 61.485 66.739 1.00 0.00
> ATOM 1730 OW HOH 189 68.765 60.471 69.225 1.00 0.00
> ATOM 1731 HW1 HOH 189 69.581 60.471 69.802 1.00 0.00
> ATOM 1732 HW2 HOH 189 68.765 59.655 68.648 1.00 0.00
> ATOM 1733 CAB LIG 190 71.884 63.353 62.792 1.00 0.00
> ATOM 1734 HAB LIG 190 70.812 63.372 62.596 1.00 0.00
> ........................................
> ......................
> ........
> ATOM 1746 HAI LIG 190 72.792 64.517 66.353 1.00 0.00
> ATOM 1747 OW SOL 191 5.690 12.751 11.651 1.00 0.00
> ATOM 1748 HW1 SOL 191 4.760 12.681 11.281 1.00 0.00
> ATOM 1749 HW2 SOL 191 5.800 13.641 12.091 1.00 0.00
> ATOM 1750 OW SOL 192 15.551 15.111 7.030 1.00 0.00
> ATOM 1751 HW1 SOL 192 14.981 14.951 7.840 1.00 0.00
> .....
> ..............
>
> What could be the problem??
>
It is exactly what I said; you've proven it. You have solvent, ligand, then
solvent. To use genion (as the program prints out at the prompt) you must have
a *continuous* group of solvent in order to embed ions. If you re-arrange the
coordinate file and [molecules] section of the topology, you can achieve this.
-Justin
> thanks in advance.
> MIguel.
>
>
>
> 2010/1/26 <gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>
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> Today's Topics:
>
> 1. Re: the solvent group SOL is not continuous (Justin A. Lemkul)
> 2. Potential Energy (Yanmei Song)
> 3. RE?: gmx-users Digest, Vol 69, Issue 132 (ABEL Stephane 175950)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 26 Jan 2010 16:30:07 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> Subject: Re: [gmx-users] the solvent group SOL is not continuous
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4B5F5EDF.4080108 at vt.edu <mailto:4B5F5EDF.4080108 at vt.edu>>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Miguel Quiliano Meza wrote:
> > *Hi everyone.
> >
> > I have a problem when I try to run GENION, GROMACS says:
> > *
> > WARNING: turning of free energy, will use lambda=0
> > Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision)
> > Using a coulomb cut-off of 0.9 nm
> > Will try to add 0 Na ions and 15 NA+ ions.
> > Select a continuous group of solvent molecules
> > Opening library file /usr/share/gromacs/top/
> > aminoacids.dat
> > Group 0 ( System) has 275439 elements
> > Group 1 ( Protein) has 1722 elements
> > Group 2 ( Protein-H) has 1371 elements
> > Group 3 ( C-alpha) has 185 elements
> > Group 4 ( Backbone) has 555 elements
> > Group 5 ( MainChain) has 741 elements
> > Group 6 (MainChain+Cb) has 909 elements
> > Group 7 ( MainChain+H) has 921 elements
> > Group 8 ( SideChain) has 801 elements
> > Group 9 ( SideChain-H) has 630 elements
> > Group 10 ( Prot-Masses) has 1722 elements
> > Group 11 ( Non-Protein) has 273717 elements
> > Group 12 ( ZN) has 1 elements
> > Group 13 ( SOL) has 273702 elements
> > Group 14 ( LIG) has 14 elements
> > Group 15 ( Other) has 273717 elements
> > Select a group: 13
> > Selected 13: 'SOL'
> >
> > -------------------------------------------------------
> > Program genion, VERSION 3.3.3
> > Source code file: ../../../../src/tools/gmx_genion.c, line: 429
> >
> > Fatal error:
> > The solvent group SOL is not continuous: index[9]=1732,
> index[10]=1747
> > -------------------------------------------------------
> >
> > "Bad As This Shit Is, This Shit Ain't As Bad As You Think It Is."
> > (Jackie Brown)
> >
> > *I do not know the reason,the number of residues in top file and pdb
> > file are the same. The only warning that I saw was when I ran grompp:
> > *
> > WARNING 1 [file 1x8a.top, line unknown]:
> > The largest charge group contains 11 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.
> >
> > *Coincidentally they are some of the atomos of my ligand*
> > *
> > I have been reading the web and no-one says nothing about it. I
> would be
> > very grateful if someone can help me or give me advices.
> >
>
> Look at your coordinate file. Do you have two separate blocks of
> solvent, like
> crystal waters and then solvent added by genbox (after your zinc and
> ligand,
> perhaps)?
>
> -Justin
>
> > Best Regards
> > MIguel Quiliano*
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 26 Jan 2010 14:49:40 -0700
> From: Yanmei Song <ysong30 at asu.edu <mailto:ysong30 at asu.edu>>
> Subject: [gmx-users] Potential Energy
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID:
> <d6421a761001261349o49b01994j64acf046d9ea08e9 at mail.gmail.com
> <mailto:d6421a761001261349o49b01994j64acf046d9ea08e9 at mail.gmail.com>>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Users:
>
> I am in the process of setting up a new system. I have a
> 8.0*8.0*8.0 nm3
> system which include 27800 molecules. When the system approach
> equilibrium,
> I found the potential energy is +3e5 (big positive number). Is this
> normal?
> Since based on my experience, for systems in such size, the
> potential energy
> is usually a big negative number? Does this mean that my force field
> parameter or molecule structure have problems? Thanks in advance!
>
> --
> Yanmei Song
> Ph.D. Candidate
> Department of Chemical Engineering
> Arizona State University
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> ------------------------------
>
> Message: 3
> Date: Tue, 26 Jan 2010 22:54:36 +0100
> From: "ABEL Stephane 175950" <Stephane.ABEL at cea.fr
> <mailto:Stephane.ABEL at cea.fr>>
> Subject: [gmx-users] RE?: gmx-users Digest, Vol 69, Issue 132
> To: <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> Message-ID:
> <F654B3EE96986E4B8DC6EF0919C88DA32AB43B at LODERI.intra.cea.fr
> <mailto:F654B3EE96986E4B8DC6EF0919C88DA32AB43B at LODERI.intra.cea.fr>>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thanks Justin
>
> Indeed, It worked !!!
>
> In french, one says: "je ne dormirai pas idiot ce soir".
>
> Stéphane
>
>
>
> >Thank you Roland for your response
>
> >I have effectively downloaded from the
> >http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz, the HEAD version
> >of gmx Unfortunately, the unpacked directory does not contain a
> >configure file, I have only an configure.ac <http://configure.ac>.
>
> >So my question is: how to obtain a fully fonctional version of 4.1
> >without using git
>
> >Thank you for your response
> >
> > Hi,
> >
> > there is currently no web-interface on the official git server. Thus
> > repo.or.wz is probably the best solution.
> > I checked that
> http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz is
> > up-to-date.
> >
> > Roland
> >
> > On Tue, Feb 23, 2010 at 8:31 AM, intra\sa175950
> <stephane.abel at cea.fr <mailto:stephane.abel at cea.fr>>wrote:
> >
> >
> >> Hi all,
> >>
> >>
> >>
> >> For a future project, I would like to use gromacs for
> simulations with the
> >> CHARMM force field. I am aware that the CHARMM ff is not yet
> "officially"
> >> supported by gromacs, even if a paper about this port will be
> published
> >> soon. By reading the mailing list, I understand that a beta
> version of
> >> gmx4.1 is available for testing from the git depositary. I have
> tried to use
> >> git, but since I am behind a firewall, I cannot easily access to the
> >> depositary. I have tried to obtain a previous from
> >> http://repo.or.cz/w/gromacs.git through the master branch but I
> am not
> >> sure that the file downloaded was the latest version. Therefore,
> my question
> >> is how to obtain the latest version of pre gmx4.1 without using
> git ?
> >>
> >>
> >>
> >> Thank you for your help
> >>
> >>
> >>
> >> Stéphane
> >>
> >> --
> >> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search
> before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>
> >>
> >
> >
> >
> >
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 26 Jan 2010 14:00:00 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> Subject: Re: [gmx-users] Re: Obtain a pre-version of gromacs 4.1
> without git
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4B5F3BB0.1000801 at vt.edu <mailto:4B5F3BB0.1000801 at vt.edu>>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> Stephane Abel wrote:
> > Thank you Roland for your response
> >
> > I have effectively downloaded from the
> > http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz, the HEAD
> version
> > of gmx Unfortunately, the unpacked directory does not contain a
> > configure file, I have only an configure.ac <http://configure.ac>.
> >
> > So my question is: how to obtain a fully fonctional version of 4.1
> > without using git
> >
>
> In the code you downloaded, there should be a script called
> "bootstrap" which
> you can execute to generate the configure file.
>
> -Justin
>
> > Thank you for your response
> >>
> >> Hi,
> >>
> >> there is currently no web-interface on the official git server. Thus
> >> repo.or.wz is probably the best solution.
> >> I checked that
> http://repo.or.cz/w/gromacs.git/snapshot/HEAD.tar.gz is
> >> up-to-date.
> >>
> >> Roland
> >>
> >> On Tue, Feb 23, 2010 at 8:31 AM, intra\sa175950
> >> <stephane.abel at cea.fr <mailto:stephane.abel at cea.fr>>wrote:
> >>
> >>
> >>> Hi all,
> >>>
> >>>
> >>>
> >>> For a future project, I would like to use gromacs for simulations
> >>> with the
> >>> CHARMM force field. I am aware that the CHARMM ff is not yet
> >>> "officially"
> >>> supported by gromacs, even if a paper about this port will be
> published
> >>> soon. By reading the mailing list, I understand that a beta
> version of
> >>> gmx4.1 is available for testing from the git depositary. I have
> tried
> >>> to use
> >>> git, but since I am behind a firewall, I cannot easily access
> to the
> >>> depositary. I have tried to obtain a previous from
> >>> http://repo.or.cz/w/gromacs.git through the master branch but I
> am not
> >>> sure that the file downloaded was the latest version. Therefore, my
> >>> question
> >>> is how to obtain the latest version of pre gmx4.1 without using
> git ?
> >>>
> >>>
> >>>
> >>> Thank you for your help
> >>>
> >>>
> >>>
> >>> Stéphane
> >>>
> >>> --
> >>> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> Please search the archive at http://www.gromacs.org/search before
> >>> posting!
> >>> Please don't post (un)subscribe requests to the list. Use the
> >>> www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>>
> >>>
> >>
> >>
> >>
> >>
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 27 Jan 2010 08:09:47 +1100
> From: "Dallas B. Warren" <Dallas.Warren at pharm.monash.edu.au
> <mailto:Dallas.Warren at pharm.monash.edu.au>>
> Subject: RE: [gmx-users] Ligand coming out while trying Drug-enzyme
> tutorial
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID:
> <89907EA1DCFB7548A431C13A270F9DD508FD800E at prk-exch-01.vcp.local>
> Content-Type: text/plain; charset="us-ascii"
>
> So, what EXACTLY are you doing?
>
>
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at pharm.monash.edu.au
> <mailto:dallas.warren at pharm.monash.edu.au>
> +61 3 9903 9167
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble
> a nail.
>
>
>
> From: gmx-users-bounces at gromacs.org
> <mailto:gmx-users-bounces at gromacs.org>
> [mailto:gmx-users-bounces at gromacs.org
> <mailto:gmx-users-bounces at gromacs.org>] On Behalf Of vivek sharma
> Sent: Monday, 25 January 2010 7:38 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Ligand coming out while trying Drug-enzyme
> tutorial
>
>
>
> HI Tsjerk,
> Thanks for your reply. But, I can't see if it is going suddenly or
> gradually.
> What i can see is the ligand is away from the molecule after editing the
> gro file with PRODRG output.
>
> It seems liek PRODRG has modified the co-ordinates that places ligand
> away from the protein.
>
> ~Vivek
>
> 2010/1/25 Tsjerk Wassenaar <tsjerkw at gmail.com
> <mailto:tsjerkw at gmail.com>>
>
> Hi Vivek,
>
>
> > Now when I am processing the modified .gro file to generate box, the
> ligand
> > and cofactor are going away from the protein molecule and I am not
> able to
> > analyze the complex.
>
> Gradually going away, or suddenly jumping?
>
> In the latter case, read up on periodic boundary conditions.
>
> Tsjerk
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> Computational Chemist
> Medicinal Chemist
> Neuropharmacologist
> --
>
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
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> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
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>
> Message: 5
> Date: Tue, 26 Jan 2010 16:26:09 -0500
> From: Miguel Quiliano Meza <rifaximina at gmail.com
> <mailto:rifaximina at gmail.com>>
> Subject: [gmx-users] the solvent group SOL is not continuous
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Message-ID:
> <6c2f55e31001261326w7d3a2588wf577aa5b3f6614a3 at mail.gmail.com
> <mailto:6c2f55e31001261326w7d3a2588wf577aa5b3f6614a3 at mail.gmail.com>>
> Content-Type: text/plain; charset="iso-8859-1"
>
> *Hi everyone.
>
> I have a problem when I try to run GENION, GROMACS says:
> *
> WARNING: turning of free energy, will use lambda=0
> Reading file 1x8a_solvatada.tpr, VERSION 3.3.3 (single precision)
> Using a coulomb cut-off of 0.9 nm
> Will try to add 0 Na ions and 15 NA+ ions.
> Select a continuous group of solvent molecules
> Opening library file /usr/share/gromacs/top/
> aminoacids.dat
> Group 0 ( System) has 275439 elements
> Group 1 ( Protein) has 1722 elements
> Group 2 ( Protein-H) has 1371 elements
> Group 3 ( C-alpha) has 185 elements
> Group 4 ( Backbone) has 555 elements
> Group 5 ( MainChain) has 741 elements
> Group 6 (MainChain+Cb) has 909 elements
> Group 7 ( MainChain+H) has 921 elements
> Group 8 ( SideChain) has 801 elements
> Group 9 ( SideChain-H) has 630 elements
> Group 10 ( Prot-Masses) has 1722 elements
> Group 11 ( Non-Protein) has 273717 elements
> Group 12 ( ZN) has 1 elements
> Group 13 ( SOL) has 273702 elements
> Group 14 ( LIG) has 14 elements
> Group 15 ( Other) has 273717 elements
> Select a group: 13
> Selected 13: 'SOL'
>
> -------------------------------------------------------
> Program genion, VERSION 3.3.3
> Source code file: ../../../../src/tools/gmx_genion.c, line: 429
>
> Fatal error:
> The solvent group SOL is not continuous: index[9]=1732, index[10]=1747
> -------------------------------------------------------
>
> "Bad As This Shit Is, This Shit Ain't As Bad As You Think It Is."
> (Jackie
> Brown)
>
> *I do not know the reason,the number of residues in top file and pdb
> file
> are the same. The only warning that I saw was when I ran grompp:
> *
> WARNING 1 [file 1x8a.top, line unknown]:
> The largest charge group contains 11 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.
>
> *Coincidentally they are some of the atomos of my ligand*
> *
> I have been reading the web and no-one says nothing about it. I would be
> very grateful if someone can help me or give me advices.
>
> Best Regards
> MIguel Quiliano*
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> posting!
>
> End of gmx-users Digest, Vol 69, Issue 133
> ******************************************
>
>
--
========================================
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
========================================
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