[gmx-users] Re: OXY not found
Andy Torres
torand2000 at gmail.com
Fri Mar 6 19:30:21 CET 2009
Thanks Justin and Chris for the fast answer! I follow the Chris instructions
but modifying the molecule name '[ OTWO ]' for '[ OTW ]' because
otherwise gromacs error appears (there are other names with 4 letters code,
I don't know why these is not valid). But it's working now!
Andy
2009/3/5 <gmx-users-request at gromacs.org>
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> Today's Topics:
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> 1. problem in running grompp (victor doss)
> 2. problem running grompp - error message here (victor doss)
> 3. Re: problem running grompp - error message here
> (Justin A. Lemkul)
> 4. OXY not found (Andy Torres)
> 5. Re: OXY not found (Justin A. Lemkul)
> 6. distance restraints for alpha helix (abhigna polavarapu)
> 7. OXY not found (Chris Neale)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 5 Mar 2009 17:32:12 +0000
> From: victor doss <victordoss64 at hotmail.com>
> Subject: [gmx-users] problem in running grompp
> To: <gmx-users at gromacs.org>
> Message-ID: <BAY133-W1010815281DF3AC24A8CC4D3A40 at phx.gbl>
> Content-Type: text/plain; charset="windows-1252"
>
>
> Hello,
>
> when I run grompp I get the following error message always. Whoever has a
> correct fix to get rid of this error message and get the actual result,
> Please suggest.
>
> Thanking you
>
>
> Dr. Victor A. Doss
>
>
> _________________________________________________________________
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> Message: 2
> Date: Thu, 5 Mar 2009 17:34:59 +0000
> From: victor doss <victordoss64 at hotmail.com>
> Subject: [gmx-users] problem running grompp - error message here
> To: <gmx-users at gromacs.org>
> Message-ID: <BAY133-W324784EED131FBFB366F6BD3A40 at phx.gbl>
> Content-Type: text/plain; charset="windows-1252"
>
>
> Hello,
>
> when I run grompp I get the following error message
> always. Whoever has a correct fix to get rid of this error message and
> get the actual result, Please suggest.
>
> Thanking you
>
>
> Dr. Victor A. Doss
>
>
> processing topology...
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
> Excluding 3 bonded neighbours for Protein_A 1
> Excluding 2 bonded neighbours for SOL 82
> Excluding 2 bonded neighbours for SOL 9514
> NOTE:
> System has non-zero total charge: 8.000000e+00
>
> processing coordinates...
> double-checking input for internal consistency...
>
> -------------------------------------------------------
> Program grompp, VERSION 3.3.3
> Source code file: ../../../../src/kernel/grompp.c, line: 1134
>
> Fatal error:
> There were 3 error(s) processing your input
> -------------------------------------------------------
>
> "Can't You Make This Thing Go Faster ?" (Black Crowes)
>
> dv at dv-laptop:~/g
>
>
> _________________________________________________________________
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> ------------------------------
>
> Message: 3
> Date: Thu, 05 Mar 2009 13:02:29 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] problem running grompp - error message here
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <49B013B5.6030207 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> victor doss wrote:
> > Hello,
> >
> > when I run grompp I get the following error message always. Whoever
> > has a correct fix to get rid of this error message and get the actual
> > result, Please suggest.
> >
> > Thanking you
> >
> >
> > Dr. Victor A. Doss
> >
> >
> > processing topology...
> > Generated 332520 of the 332520 non-bonded parameter combinations
> > Generating 1-4 interactions: fudge = 0.5
> > Generated 332520 of the 332520 1-4 parameter combinations
> > Excluding 3 bonded neighbours for Protein_A 1
> > Excluding 2 bonded neighbours for SOL 82
> > Excluding 2 bonded neighbours for SOL 9514
> > NOTE:
> > System has non-zero total charge: 8.000000e+00
> >
> > processing coordinates...
> > double-checking input for internal consistency...
> >
> > -------------------------------------------------------
> > Program grompp, VERSION 3.3.3
> > Source code file: ../../../../src/kernel/grompp.c, line: 1134
> >
> > Fatal error:
> > There were 3 error(s) processing your input
> > -------------------------------------------------------
> >
> > "Can't You Make This Thing Go Faster ?" (Black Crowes)
> >
>
> The error messages themselves are actually printed above in the grompp
> output.
> Those are what you need to solve. Search the list archive for the error
> messages, as well as the wiki site.
>
> -Justin
>
> > dv at dv-laptop:~/g
> >
> >
> > ------------------------------------------------------------------------
> > Twice the fun— Share photos while you chat with Windows Live Messenger.
> > <http://www.microsoft.com/india/windows/windowslive/messenger.aspx>
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
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> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 5 Mar 2009 16:17:27 -0200
> From: Andy Torres <torand2000 at gmail.com>
> Subject: [gmx-users] OXY not found
> To: gmx-users at gromacs.org
> Message-ID:
> <2d35fa4f0903051017q71288fb4l4d8b5d9f0e024ec8 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi, I run pdb2gmx (with all the ff that Gromacs bring by default) on
> myoglobin (1A6M.pdb) wich I get from the "protein data bank". and I got the
> following
>
> Fatal error:
> Residue 'OXY' not found in residue topology database
>
> I check the ff and I did not found the oxigen molecule.
> I saw that somebody allready use this molecule in the mailing list:
>
> On Tue, 18 Jun 2002, Valentin Gogonea
>
> Is there a chance to contact him?
> Is this molecule in any other ff?
> How can I fix this?
> How can I take the OXI and SO4 molecules out of my .pdb file without making
> mistakes?
> Hopping to be clear.
> Thanks in advance
>
> Andy
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> ------------------------------
>
> Message: 5
> Date: Thu, 05 Mar 2009 13:32:22 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] OXY not found
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <49B01AB6.905 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Andy Torres wrote:
> > Hi, I run pdb2gmx (with all the ff that Gromacs bring by default) on
> > myoglobin (1A6M.pdb) wich I get from the "protein data bank". and I got
> > the following
> >
> > Fatal error:
> > Residue 'OXY' not found in residue topology database
> >
> > I check the ff and I did not found the oxigen molecule.
> > I saw that somebody allready use this molecule in the mailing list:
> >
> > On Tue, 18 Jun 2002, Valentin Gogonea
> >
> > Is there a chance to contact him?
>
> If this individual still subscribes to this list after all these years, you
> may
> get a reply.
>
> > Is this molecule in any other ff?
>
> Not typically. The force fields included in Gromacs are generally designed
> for
> condensed-phase species like proteins, nucleic acids, and small organics.
>
> > How can I fix this?
>
> That depends on your definition of "fix." If you need to simulate
> myoglobin
> with oxygen bound, you may be in for the difficult (read: very advanced!)
> topic
> of parameterization:
>
> http://wiki.gromacs.org/index.php/Parameterization
>
> With special consideration of the fact that the oxygen is probably bound to
> heme:
>
> http://wiki.gromacs.org/index.php/Exotic_Species
>
> > How can I take the OXI and SO4 molecules out of my .pdb file without
> > making mistakes?
>
> That depends on your definition of "mistake." Whether or not these
> molecules
> are relevant to your dynamics is a decision only you can make.
>
> -Justin
>
> > Hopping to be clear.
> > Thanks in advance
> >
> > Andy
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.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.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 5 Mar 2009 13:41:50 -0500
> From: abhigna polavarapu <abhignap at gmail.com>
> Subject: [gmx-users] distance restraints for alpha helix
> To: gmx-users at gromacs.org
> Message-ID:
> <feabd7290903051041w207fbf65v2383126bc3c5e39d at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear all,
> I am trying to rebuild the alpha helix of one the chains
> which got destroyed during the simulation. I found that we can do that
> by distance restraints. So my question what is a better way of
> distance restraints i.e should I restrain the hydrogen bonds of the
> helix or any particular bond distances. I was not clear when I read
> the chapter 4 in manual, what type' should I use for this, are these
> parameterized anywhere because the manual says type' should be 1 for
> bonds but for hydrogen bonds it varies from 0-2. I found an exercise
> by David van der Spoel
>
> http://www.csc.fi/english/research/sciences/chemistry/courses/gmx2004/exercises/index_html
> but could not access the files, so I was not clear what atoms did he
> use for restraints.
>
> Thank you
> abhigna
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 05 Mar 2009 13:58:18 -0500
> From: Chris Neale <chris.neale at utoronto.ca>
> Subject: [gmx-users] OXY not found
> To: gmx-users at gromacs.org
> Message-ID: <49B020CA.9010106 at utoronto.ca>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Andy,
>
> I did some work on molecular oxygen back in 2006. There have been a few
> requests for molecular oxygen parameters so I decided to
> dig them up. Here are the parameters that I used for that work. I leave it
> to you to read the relevant papers and decide if
> these parameters are appropriate for your simulations.
>
> Note that I went with an epsilon value that I converted myself from Fisher
> and Lago (3.71000e-01) and considered
> the value used by Marrink and Berendsen (3.63000e-01) to have been
> incorrectly converted. However, we never did publish our
> simulations so I can't give you a reference for that discrepancy, which, to
> my knowledge, has not previously been reported.
>
> After modifying the files as I outline below, you will need to rename your
> oxygen residue and atomic names to match and then it
> should respond properly to a run through pdb2gmx.
>
> It probably makes a lot more sense to create an otwo.itp file, but I did
> this in my early gromacs days and didn;t know how
> to do that then. I am leaving the instructions intact as I did it at the
> time since that is easier for me.
>
> For a separate set of parameters, you might look at Bembenek and Rice JCP
> vol 113 #6 p. 2354-9 and Bembenek JCP 124 (2006).
> I did not decide that the Fisher and Lago parameters were "better", I just
> picked them since they had previously been used in our lab:
> Al-Abdul-Wahid MS, Yu CH, Batruch I, Evanics F, Pomès R, Prosser RS. "A
> combined NMR and molecular dynamics study of the transmembrane
> solubility and diffusion rate profile of dioxygen in lipid bilayers."
> Biochemistry. 2006 Sep 5;45(35):10719-28.
> Although that paper utilized the values directly from Marrink and
> Berendsen.
>
>
> ## Add to ffX.atp:
> ; Added by Chris Neale March 16 2006 based on
> ; 1) Fisher and Lago J. Chem. Phys. 78(9), 1 May 1983
> ; 2) Marrink and Berendsen J. Phys. Chem. 1996, 100, 16729-16738
> OOT 15.99940 ; O in nitro R-NO2
>
> ## Add to ffX.rtp:
> [ OTWO ]
> ; Added by Chris Neale March 16 2005 based on
> ; 1) Fisher and Lago J. Chem. Phys. 78(9), 1 May 1983
> ; 2) Marrink and Berendsen J. Phys. Chem. 1996, 100, 16729-16738
> [ atoms ]
> OOA OOT 0.00 0
> OOB OOT 0.00 0
> [ bonds ]
> OOA OOB
>
> ## Add to ffXbon.itp
> ; Added by Chris Neale March 16 2005 based on
> ; 1) Fisher and Lago J. Chem. Phys. 78(9), 1 May 1983
> ; 2) Marrink and Berendsen J. Phys. Chem. 1996, 100, 16729-16738
> [ bondtypes ]
> ; i j func b0 kb
> OOT OOT 1 0.10160 659840.
> ;[ constrainttypes ]
> ;[ angletypes ]
> ;[ dihedraltypes ]
>
> ## Add to ffXnb.itp:
> ; Added by Chris Neale March 16 2006 based on
> ; 1) Fisher and Lago J. Chem. Phys. 78(9), 1 May 1983
> ; 2) Marrink and Berendsen J. Phys. Chem. 1996, 100, 16729-16738
> ; name bond_type mass charge ptype sigma epsilon
> OOT OOT 1 15.99940 0.000 A 3.09000e-01
> 3.71000e-01
>
> Chris.
>
>
> -- original message --
>
> Hi, I run pdb2gmx (with all the ff that Gromacs bring by default) on
> myoglobin (1A6M.pdb) wich I get from the "protein data bank". and I got the
> following
>
> Fatal error:
> Residue 'OXY' not found in residue topology database
>
> I check the ff and I did not found the oxigen molecule.
> I saw that somebody allready use this molecule in the mailing list:
>
> On Tue, 18 Jun 2002, Valentin Gogonea
>
> Is there a chance to contact him?
> Is this molecule in any other ff?
> How can I fix this?
> How can I take the OXI and SO4 molecules out of my .pdb file without making
> mistakes?
> Hopping to be clear.
> Thanks in advance
>
> Andy
>
>
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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>
> End of gmx-users Digest, Vol 59, Issue 51
> *****************************************
>
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