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-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
Date: Mon, Aug 23, 2010 at 7:00 AM
Subject: gmx-users Digest, Vol 76, Issue 113
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
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Today's Topics:
1. Metallic boundary conditions (poj...@icp.uni-stuttgart.de
<mailto:poj...@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: poj...@icp.uni-stuttgart.de <mailto:poj...@icp.uni-stuttgart.de>
Subject: [gmx-users] Metallic boundary conditions
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Message-ID:
<3e5fe7757a687609503cad715e2a5d15.squir...@www.icp.uni-stuttgart.de
<mailto:3e5fe7757a687609503cad715e2a5d15.squir...@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 <fil...@ufabc.edu.br <mailto:fil...@ufabc.edu.br>>
Subject: [gmx-users] Charmm to Gromacs: Polyols force field
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Message-ID:
<aanlktikqtlshdgqsmprykc0x0fjiq+c_ydzcm6pke...@mail.gmail.com
<mailto:aanlktikqtlshdgqsmprykc0x0fjiq%2bc_ydzcm6pke...@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" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] Charmm to Gromacs: Polyols force field
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <4c71627f.1000...@vt.edu <mailto:4c71627f.1000...@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 <wadoodbiochem...@hotmail.com
<mailto:wadoodbiochem...@hotmail.com>>
Subject: [gmx-users] PMF
To: gromacs <gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
Message-ID: <bay121-w7c84bc40d94bebf163356d0...@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:wadoodbiochem...@hotmail.com
<mailto:email%3awadoodbiochem...@hotmail.com>
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Message: 5
Date: Mon, 23 Aug 2010 09:56:26 +0200
From: Sander Pronk <pr...@cbr.su.se <mailto:pr...@cbr.su.se>>
Subject: Re: [gmx-users] please, how edr data is xdr packed?
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <31d44996-834b-4f78-8880-81320fe9e...@cbr.su.se
<mailto:31d44996-834b-4f78-8880-81320fe9e...@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@gromacs.org
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