[gmx-users] Charmm to Gromacs: Polyols force field [Justin]
Eudes Fileti
fileti at ufabc.edu.br
Mon Aug 23 14:07:12 CEST 2010
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.
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>
> Date: Mon, Aug 23, 2010 at 7:00 AM
> Subject: gmx-users Digest, Vol 76, Issue 113
> To: gmx-users at gromacs.org
>
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> Today's Topics:
>
> 1. Metallic boundary conditions (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
> Subject: [gmx-users] Metallic boundary conditions
> To: gmx-users at gromacs.org
> Message-ID:
> <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>
> Subject: [gmx-users] Charmm to Gromacs: Polyols force field
> To: gmx-users at gromacs.org
> Message-ID:
> <AANLkTikQtLsHdgQsMprykc0X0fjiQ+C_ydzcM6pKE5OV at mail.gmail.com<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>
> Subject: Re: [gmx-users] Charmm to Gromacs: Polyols force field
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <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 | (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>
> Subject: [gmx-users] PMF
> To: gromacs <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 <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>
> Subject: Re: [gmx-users] please, how edr data is xdr packed?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <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
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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