[gmx-users] Charmm to Gromacs: Polyols force field [Justin]
Justin A. Lemkul
jalemkul at vt.edu
Mon Aug 23 14:14:35 CEST 2010
Eudes Fileti wrote:
> Hello Justin, thank you for answering!
> I think I already have done what you suggested when I created my
> ffbonded.itp and .rtp files.
>
> I am sending a piece of my topology and ffbonded.itp files.
> Follows also the residue from .rtp and the configuration of glycol (.gro)
> so you can consider where I might be wrong and what I still must do.
> Thanks again.
>
I appreciate the detail, but partial topologies are not useful for diagnosing
anything. As I asked before, what is on line 40 of the topology? Which
specific bond does this correspond to? What you need to determine is which bond
type should be called and why it's not being found.
-Justin
> eef
>
>
> !!! topol.top !!!
> ; Include forcefield parameters
> #include "charmm27.ff/forcefield.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> Other 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 HCP1 1 PA2 HOA 1 0.42 1.008 ;
> qtot 0.42
> 2 OC311 1 PA2 OHA 1 -0.65 15.9994 ;
> qtot -0.23
> 3 CC322 1 PA2 CA 1 0.05 12.011 ;
> qtot -0.18
> 4 HCA2 1 PA2 HA1 1 0.09 1.008 ;
> qtot -0.09
> ...
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1
> 2 3 1
> 3 4 1
> ...
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 1 4 1
> 1 5 1
> 1 6 1
> ...
>
> [ angles ]
> ; ai aj ak funct c0 c1 c2
> c3
> 1 2 3 5
> 2 3 4 5
> ...
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1 c2
> c3 c4 c5
> 1 2 3 4 9
> ...
>
>
> !!! ffbonded.itp !!!
> [ bondtypes ]
> ; i j func b0 kb
> OC311 HCP1 1 0.0960 456056.0 ; par22 OH1 H
> CC322 OC311 1 0.1420 334720.0 ; adm 11/08, glycerol
> CC322 HCA2 1 0.1111 258571.2 ; par22 HA CT2
> [ angletypes ]
> ; i j k func th0 cth ub0 cub
> HCP1 OC311 CC312 5 106.00 412.40 0.0 0.00
> ; og 1/06 EtOH IR fit
> [ dihedraltypes ]
> ; i j k l func phi0 cp mult
> HCP1 OC311 CC322 HCA2 9 0.0 0.75 3 ; og methanol
>
> !!! file.rtp !!!
>
> [ PA2 ]
> ; Glycol
> [ atoms ]
> HOA HCP1 0.420 1
> OHA OC311 -0.650 1
> CA CC322 0.050 1
> HA1 HCA2 0.090 1
> HA2 HCA2 0.090 1
> CB CC322 0.050 2
> HB1 HCA2 0.090 2
> HB2 HCA2 0.090 2
> OHB OC311 -0.650 2
> HOB HCP1 0.420 2
>
> [ bonds ]
> OHA HOA
> OHA CA
> CA HA1
> CA HA2
> CB CA
> CB HB1
> CB HB2
> OHB CB
> HOB OHB
>
> !!! conf.gro !!!
> GROningen MAchine for Chemical Simulation
> 10
> 1PA2 HOA 1 -0.248 -0.048 0.000
> 1PA2 OHA 2 -0.177 0.017 0.000
> 1PA2 CA 3 -0.052 -0.052 0.000
> 1PA2 HA1 4 -0.041 -0.115 0.089
> 1PA2 HA2 5 -0.041 -0.115 -0.089
> 1PA2 CB 6 0.057 0.054 0.000
> 1PA2 HB1 7 0.046 0.117 -0.089
> 1PA2 HB2 8 0.046 0.117 0.089
> 1PA2 OHB 9 0.182 -0.015 0.000
> 1PA2 HOB 10 0.253 0.049 0.000
> 3.00000 3.00000 3.00000
>
>
> _______________________________________
> Eudes Eterno Fileti
> Centro de Ciências Naturais e Humanas
> Universidade Federal do ABC — CCNH
> Av. dos Estados, 5001
> Santo André - SP - Brasil
> CEP 09210-971
> +55.11.4996-0196
> http://fileti.ufabc.edu.br
>
>
>
>
> ---------- Forwarded message ----------
> From: ** <gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>
> Date: Mon, Aug 23, 2010 at 7:00 AM
> Subject: gmx-users Digest, Vol 76, Issue 113
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
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> Today's Topics:
>
> 1. Metallic boundary conditions (pojeda at icp.uni-stuttgart.de
> <mailto:pojeda at icp.uni-stuttgart.de>)
> 2. Charmm to Gromacs: Polyols force field (Eudes Fileti)
> 3. Re: Charmm to Gromacs: Polyols force field (Justin A. Lemkul)
> 4. PMF (abdul wadood)
> 5. Re: please, how edr data is xdr packed? (Sander Pronk)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 22 Aug 2010 17:52:46 +0200
> From: pojeda at icp.uni-stuttgart.de <mailto:pojeda at icp.uni-stuttgart.de>
> Subject: [gmx-users] Metallic boundary conditions
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Message-ID:
>
> <3e5fe7757a687609503cad715e2a5d15.squirrel at www.icp.uni-stuttgart.de
> <mailto:3e5fe7757a687609503cad715e2a5d15.squirrel at www.icp.uni-stuttgart.de>>
> Content-Type: text/plain;charset=iso-8859-1
>
>
> Hi,
>
> thank you for your answer. What is then epsilon_r ?
>
> regards.
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 22 Aug 2010 14:42:43 -0300
> From: Eudes Fileti <fileti at ufabc.edu.br <mailto:fileti at ufabc.edu.br>>
> Subject: [gmx-users] Charmm to Gromacs: Polyols force field
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Message-ID:
> <AANLkTikQtLsHdgQsMprykc0X0fjiQ+C_ydzcM6pKE5OV at mail.gmail.com
> <mailto:AANLkTikQtLsHdgQsMprykc0X0fjiQ%2BC_ydzcM6pKE5OV at mail.gmail.com>>
> Content-Type: text/plain; charset="windows-1252"
>
> Olá pessoal,
>
> Recently, McKerrel published his CHARMM force field to polyols
> (JCTC, 2009,
> 5, 1315).
> I am very interested in using it in GROMACS.
>
> For this, I began the transfer of the parameters with the following
> recipe:
>
> 1) All atom types were added to the atomtypes.atp file;
> 2) All bonded parameters (bonds, angles, ub, dihedral and impropers)
> were added to the ffbonded.itp file;
> 3) van der Waals and Coulomb parameters were inserted properly
> in ffnonbonded.itp;
> 4) The residues were created in a new file named polyols.rtp.
>
> Well, pdb2gmx works fine! It generates the restraints file (posre.itp),
> configuration file
> (conf.gro) and topology file (topol.itp). But when I run it in
> grommp, the
> default for
> parameters are not found. Something like:
>
> ERROR 6 [file topol.top, line 40]:
> No default Bond types
>
> I know I can insert the parameters by hand in each .top file
> generated by
> pdb2gmx.
> But what I need to do, so that grompp recognizes the default values
> automatically.
>
> Did I forgot some file? I'm making some mistake?
>
> Any suggestion is welcome!
>
> Muito obrigado!
> eef
>
> _______________________________________
> Eudes Eterno Fileti
> Centro de Ciências Naturais e Humanas
> Universidade Federal do ABC — CCNH
> Av. dos Estados, 5001
> Santo André - SP - Brasil
> CEP 09210-971
> +55.11.4996-0196
> http://fileti.ufabc.edu.br
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> ------------------------------
>
> Message: 3
> Date: Sun, 22 Aug 2010 13:46:39 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> Subject: Re: [gmx-users] Charmm to Gromacs: Polyols force field
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4C71627F.1000402 at vt.edu <mailto:4C71627F.1000402 at vt.edu>>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> Eudes Fileti wrote:
> > Olá pessoal,
> >
> > Recently, McKerrel published his CHARMM force field to polyols (JCTC,
> > 2009, 5, 1315).
> > I am very interested in using it in GROMACS.
> >
> > For this, I began the transfer of the parameters with the
> following recipe:
> >
> > 1) All atom types were added to the atomtypes.atp file;
> > 2) All bonded parameters (bonds, angles, ub, dihedral and impropers)
> > were added to the ffbonded.itp file;
> > 3) van der Waals and Coulomb parameters were inserted properly
> > in ffnonbonded.itp;
> > 4) The residues were created in a new file named polyols.rtp.
> >
> > Well, pdb2gmx works fine! It generates the restraints file
> (posre.itp),
> > configuration file
> > (conf.gro) and topology file (topol.itp). But when I run it in
> grommp,
> > the default for
> > parameters are not found. Something like:
> >
> > ERROR 6 [file topol.top, line 40]:
> > No default Bond types
> >
> > I know I can insert the parameters by hand in each .top file
> generated
> > by pdb2gmx.
> > But what I need to do, so that grompp recognizes the default values
> > automatically.
> >
> > Did I forgot some file? I'm making some mistake?
> >
>
> Look on line 40 of the topology and see which atoms grompp is
> complaining about.
> You likely forgot to define the parameters for that particular bond
> type.
>
> -Justin
>
> > Any suggestion is welcome!
> >
> > Muito obrigado!
> > eef
> >
> > _______________________________________
> > Eudes Eterno Fileti
> > Centro de Ciências Naturais e Humanas
> > Universidade Federal do ABC — CCNH
> > Av. dos Estados, 5001
> > Santo André - SP - Brasil
> > CEP 09210-971
> > +55.11.4996-0196
> > http://fileti.ufabc.edu.br
> >
>
> --
> ========================================
>
> 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: Mon, 23 Aug 2010 06:23:39 +0000
> From: abdul wadood <wadoodbiochemist at hotmail.com
> <mailto:wadoodbiochemist at hotmail.com>>
> Subject: [gmx-users] PMF
> To: gromacs <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> Message-ID: <BAY121-W7C84BC40D94BEBF163356D0820 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Hi, All
>
> I am trying to calculate pmf for enzyme ligand complex using the
> tutorial of umbrella sampling.
> I have successfully created the unit cell around the protein and
> have solvated. The ions were also added by genion.
> But when I run the minimization step with the command
> grompp -f minim.mdp -c solv_ions.gro -p 3JY0.top -o em.tpr
> the following error comes
>
>
> Fatal error:
> Molecule type 'NA+' contains no atoms
>
>
> I tried my best to solve the problem but could no succeeded.
> Any help to solve this problem will be highly appreciated.
> The topology file is attached.
>
> Thanks in advace
>
> Many regards
>
> Abdul Wadood,
> Research Scholar,
> Dr.Panjwani Center for Molecular Medicine and
> Drug Research,
> International Center for Chemical and
> Biological Science,
> University of Karachi, Karachi-75720, Pakistan.
> Email:wadoodbiochemist at hotmail.com
> <mailto:Email%3Awadoodbiochemist at hotmail.com>
>
>
>
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>
> Message: 5
> Date: Mon, 23 Aug 2010 09:56:26 +0200
> From: Sander Pronk <pronk at cbr.su.se <mailto:pronk at cbr.su.se>>
> Subject: Re: [gmx-users] please, how edr data is xdr packed?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <31D44996-834B-4F78-8880-81320FE9E651 at cbr.su.se
> <mailto:31D44996-834B-4F78-8880-81320FE9E651 at cbr.su.se>>
> Content-Type: text/plain; charset="us-ascii"
>
> As David said, the reading/writing is done in src/gmxlib/enxio.c,
> but you could also read edr files indirectly through gmxdump: that
> should also give you an idea of the type of information in those files.
>
>
>
> On Aug 22, 2010, at 13:14 , Alan Wilter Sousa da Silva wrote:
>
> > Hi there,
> >
> > I am trying to use python xdrlib module to read edr files but not
> knowing how the data is packed using the xdr protocol makes my work
> very difficult, if not impossible.
> >
> > Would someone kindly tell me how data is packed in the edr file?
> Or where it is the gromacs code so I can try to figure out a way?
> >
> > I've read http://tools.ietf.org/html/rfc1832.html and for
> reference, see topic "6. AN EXAMPLE OF AN XDR DATA DESCRIPTION".
> >
> > My other option would be using a parsing code to read g_energy
> output but this seems very silly.
> >
> > Many thanks in advance,
> >
> > Alan
> >
> > --
> > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> > Department of Biochemistry, University of Cambridge.
> > 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> > >>http://www.bio.cam.ac.uk/~awd28<<
> > --
> > gmx-users mailing list gmx-users at gromacs.org
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--
========================================
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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