[gmx-users] D-Ala topology for OPLSAA

Attila Borics aborics at bif12.creighton.edu
Wed Feb 5 16:02:28 CET 2003


Erik,

Yes, I expected the same, but when I try to run pos.res. dynamics it
keeps crashing after 40-500 2fs steps. I suspected my tip4p water box
too, that it's not well equilibrated, but that just worked fine in my
previous simulation....that shouldn't be the problem

Attila


On Wed, 2003-02-05 at 05:00, gmx-users-request at gromacs.org wrote:
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> Today's Topics:
> 
>    1. atom name problem between .pdb and .rtp (Paul Barrett)
>    2. SEP and HO atom type (Luciane Vieira de Mello)
>    3. Re: atom name problem between .pdb and .rtp (Anton Feenstra)
>    4. Re: SEP and HO atom type (Anton Feenstra)
>    5. Re: SEP and HO atom type - again (Luciane Vieira de Mello)
>    6. Re: SEP and HO atom type - again (Anton Feenstra)
>    7. Re: SEP and HO atom type (Luciane Vieira de Mello)
>    8. Re: SEP and HO atom type (David)
>    9. D-Ala topology for OPLSAA (Attila Borics)
>   10. Re: D-Ala topology for OPLSAA (Erik Lindahl)
> 
> --__--__--
> 
> Message: 1
> Date: Tue, 04 Feb 2003 12:12:35 +0000
> From: Paul Barrett <barrett at biop.ox.ac.uk>
> To: gmx-users at gromacs.org
> CC: barrett at biop.ox.ac.uk
> Subject: [gmx-users] atom name problem between .pdb and .rtp
> Reply-To: gmx-users at gromacs.org
> 
> I am trying to model 1FIN.pdb which contains two ATP molecules. The
> names of some of the the atoms in the .pdb file are different to those
> in the .rtp file leading to errors, e.g. in .pdb the first ATP phospohor
> atom is called "PG" and in .rtp it is called "APG".
> 
> I have edited the .pdb file to correct these differences but am left
> with a problem: the longest atom names in the .rtp file are 5 characters
> long, e.g.A01PG. In .pdb format atom names are up to 4 characters
> (columns 13-16 according to PDB webpage). When I run gromacs it
> complains that it does not recognise atom A01P. It seems to have
> truncated the 5 character name I typed in to 4 characters, as it should
> for .pdb format.
> 
> How can I fix this? Presumably this happens whenever anyone models ATP?
> 
> comments / hints very gratefully received
> 
> Paul Barrett
> 
> 
> --__--__--
> 
> Message: 2
> Date: Tue, 4 Feb 2003 10:51:15 -0300
> From: Luciane Vieira de Mello <mello at cenargen.embrapa.br>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] SEP and HO atom type
> Reply-To: gmx-users at gromacs.org
> 
> 
> Dear all,
> 
> I am using the SEP (phosphoserine) from "ffG43ap" in the
> topologies/forcefields section of gromacs.org. (mail: Graham Smith
> gmx-users at gromacs.org Tue, 17 Dec 2002 19:42:29 +0000 (GMT))
> 
> Everything was going fine, till I've tried use grompp.
> I got the following message:
> 
> Generated 182 of the 1128 non-bonded parameter combinations
> Cleaning up temporary file gromppNL5TZe
> Fatal error: Atomtype 'HO' not found!
> 
> 
> I am not sure if I am checking the right file:
> ffG43a1nb.itp
> where I tried to add the HO atomtype from ffgmx2nb.itp, including the
> pairtypes.
> 
> Any clue?
> thanks in advance,
> 
> Luciane
> 
> 
> 
> +-------------------------------------------------------------------------+
> |                  Dra. Luciane Vieira de Mello Rigden                    |
> | e-mail: mello at cenargen.embrapa.br                                       |
> | Embrapa Recursos Geneticos e Biotecnologia                              |
> | Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
> | PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
> | 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |
> +-------------------------------------------------------------------------+
> 
> 
> 
> 
> 
> --__--__--
> 
> Message: 3
> Date: Tue, 04 Feb 2003 13:57:21 +0100
> From: Anton Feenstra <feenstra at chem.vu.nl>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] atom name problem between .pdb and .rtp
> Reply-To: gmx-users at gromacs.org
> 
> Paul Barrett wrote:
> > I am trying to model 1FIN.pdb which contains two ATP molecules. The
> > names of some of the the atoms in the .pdb file are different to those
> > in the .rtp file leading to errors, e.g. in .pdb the first ATP phospohor
> > atom is called "PG" and in .rtp it is called "APG".
> > 
> > I have edited the .pdb file to correct these differences but am left
> > with a problem: the longest atom names in the .rtp file are 5 characters
> > long, e.g.A01PG. In .pdb format atom names are up to 4 characters
> > (columns 13-16 according to PDB webpage). When I run gromacs it
> > complains that it does not recognise atom A01P. It seems to have
> > truncated the 5 character name I typed in to 4 characters, as it should
> > for .pdb format.
> > 
> > How can I fix this? Presumably this happens whenever anyone models ATP?
> 
> 1) first convert .pdb to .gro; .gro *will* accept 5 character atom names,
>     and pdb2gmx will read .gro as well as .pdb
> 2) hack the .rtp to match your .pdb; Atom names in the .rtp are not refered
>     to elsewhere, internally all that matters are atom types.
> 
> 
> -- 
> Groetjes,
> 
> Anton
>   ________ ___________________________________________________________
> |        | Anton Feenstra                                            |
> | .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> | |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
> | |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
> | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> |  /  \  |-----------------------------------------------------------|
> | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
> |   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
> |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
> | (    ) |-----------------------------------------------------------|
> |  \__/  | "If You See Me Getting High, Knock Me Down"               |
> |        | (Red Hot Chili Peppers)                                   |
> |________|___________________________________________________________|
> 
> 
> --__--__--
> 
> Message: 4
> Date: Tue, 04 Feb 2003 13:59:22 +0100
> From: Anton Feenstra <feenstra at chem.vu.nl>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] SEP and HO atom type
> Reply-To: gmx-users at gromacs.org
> 
> Luciane Vieira de Mello wrote:
> [...]
> > I am not sure if I am checking the right file:
> > ffG43a1nb.itp
> > where I tried to add the HO atomtype from ffgmx2nb.itp, including the
> > pairtypes.
> 
> There is also a .atp file (for Atom TyPes), but IIRC that is only
> used by pdb2gmx and not grompp... ;-(
> 
> 
> -- 
> Groetjes,
> 
> Anton
>   ________ ___________________________________________________________
> |        | Anton Feenstra                                            |
> | .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> | |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
> | |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
> | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> |  /  \  |-----------------------------------------------------------|
> | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
> |   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
> |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
> | (    ) |-----------------------------------------------------------|
> |  \__/  | "If You See Me Getting High, Knock Me Down"               |
> |        | (Red Hot Chili Peppers)                                   |
> |________|___________________________________________________________|
> 
> 
> --__--__--
> 
> Message: 5
> Date: Tue, 4 Feb 2003 11:20:06 -0300
> From: Luciane Vieira de Mello <mello at cenargen.embrapa.br>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] SEP and HO atom type - again
> Reply-To: gmx-users at gromacs.org
> 
> 
> Dear all,
> 
> another weird thing I found was the difference between
> ffgmx2nb.itp and ffG43b1nb.itp files.
> The first one has a mass for all the atoms type, while in the second all
> the masses are set to zero.
> 
> [ atomtypes ]
> ;name        mass      charge   ptype            c6           c12
>     O    15.99940       0.000       A   0.22617E-02   0.74158E-06
>    OM    15.99940       0.000       A   0.22617E-02   0.74158E-06
>    OA    15.99940       0.000       A   0.22617E-02   0.15062E-05
> 
> while:
> 
> [ atomtypes ]
> ;name        mass      charge   ptype            c6           c12
>     O     0.000      0.000     A  0.0022619536  7.4149321e-07
>    OM     0.000      0.000     A  0.0022619536  7.4149321e-07
>    OA     0.000      0.000     A  0.0022619536  1.505529e-06
>    OW     0.000      0.000     A  0.0026173456  2.634129e-06
> 
> 
> any idea?
> 
> thanks again
> Luciane
> 
> 
> +-------------------------------------------------------------------------+
> |                  Dra. Luciane Vieira de Mello Rigden                    |
> | e-mail: mello at cenargen.embrapa.br                                       |
> | Embrapa Recursos Geneticos e Biotecnologia                              |
> | Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
> | PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
> | 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |
> +-------------------------------------------------------------------------+
> 
> 
> 
> 
> 
> --__--__--
> 
> Message: 6
> Date: Tue, 04 Feb 2003 15:36:09 +0100
> From: Anton Feenstra <feenstra at chem.vu.nl>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] SEP and HO atom type - again
> Reply-To: gmx-users at gromacs.org
> 
> Luciane Vieira de Mello wrote:
> > Dear all,
> > 
> > another weird thing I found was the difference between
> > ffgmx2nb.itp and ffG43b1nb.itp files.
> > The first one has a mass for all the atoms type, while in the second all
> > the masses are set to zero.
> [...]
> 
> Yes: for the Gromos forcefield (ffG43*) the masses of atoms are defined
> in the .rtp entries, or in the molecule topologies themselves. For the
> Gromacs forcefields (ffgmx*), they are defined for the atom types.
> Still, Gromacs expects a mass field in the atom type definition, so they
> are set to 0 (for the ffG43*nb.itp)
> 
> 
> -- 
> Groetjes,
> 
> Anton
>   ________ ___________________________________________________________
> |        | Anton Feenstra                                            |
> | .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> | |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
> | |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
> | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> |  /  \  |-----------------------------------------------------------|
> | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
> |   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
> |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
> | (    ) |-----------------------------------------------------------|
> |  \__/  | "If You See Me Getting High, Knock Me Down"               |
> |        | (Red Hot Chili Peppers)                                   |
> |________|___________________________________________________________|
> 
> 
> --__--__--
> 
> Message: 7
> Date: Tue, 4 Feb 2003 18:03:12 -0300
> From: Luciane Vieira de Mello <mello at cenargen.embrapa.br>
> To: Anton Feenstra <feenstra at chem.vu.nl>
> cc: gmx-users at gromacs.org
> Subject: Re: [gmx-users] SEP and HO atom type
> Reply-To: gmx-users at gromacs.org
> 
> Dear Anton,
> 
> Thanks for you help.
> I got your two mails, but unfortunately I haven't managed to solve the
> problem yet.
> What exactly should I do in order to have the HO atom type when I run
> grompp?
> In fact I have used :
> 
> [phospho]$ pdb2gmx -f phosphoserine.pdb
> 
> choose the new option:  number 5
>  0: Gromacs Forcefield (see manual)
>  1: Gromacs Forcefield with all hydrogens (proteins only)
>  2: GROMOS96 43a1 Forcefield (official distribution)
>  3: GROMOS96 43b1 Vacuum Forcefield (official distribution)
>  4: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
>  5: ffG43a1 with SEP, TPO and PTR
> 
> and chose ffG43a1 with SEP, TPO and PTR for pdb2gmx,
> 
> Why should grompp not work when pdb2gmx was fine?  grompp is working with
> the output of pdb2gmx! (.top)
> 
> thanks in advance
> 
> +-------------------------------------------------------------------------+
> |                  Dra. Luciane Vieira de Mello Rigden                    |
> | e-mail: mello at cenargen.embrapa.br                                       |
> | Embrapa Recursos Geneticos e Biotecnologia                              |
> | Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
> | PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
> | 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |
> +-------------------------------------------------------------------------+
> 
> 
> 
> On Tue, 4 Feb 2003, Anton Feenstra wrote:
> 
> > Luciane Vieira de Mello wrote:
> > [...]
> > > I am not sure if I am checking the right file:
> > > ffG43a1nb.itp
> > > where I tried to add the HO atomtype from ffgmx2nb.itp, including the
> > > pairtypes.
> >
> > There is also a .atp file (for Atom TyPes), but IIRC that is only
> > used by pdb2gmx and not grompp... ;-(
> >
> >
> > --
> > Groetjes,
> >
> > Anton
> >   ________ ___________________________________________________________
> > |        | Anton Feenstra                                            |
> > | .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> > | |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
> > | |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
> > | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> > |  /  \  |-----------------------------------------------------------|
> > | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> > |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
> > |   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
> > |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
> > | (    ) |-----------------------------------------------------------|
> > |  \__/  | "If You See Me Getting High, Knock Me Down"               |
> > |        | (Red Hot Chili Peppers)                                   |
> > |________|___________________________________________________________|
> >
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> >
> 
> 
> 
> --__--__--
> 
> Message: 8
> Subject: Re: [gmx-users] SEP and HO atom type
> From: David <spoel at xray.bmc.uu.se>
> To: gmx-users at gromacs.org
> Date: 04 Feb 2003 20:43:06 +0100
> Reply-To: gmx-users at gromacs.org
> 
> On Tue, 2003-02-04 at 22:03, Luciane Vieira de Mello wrote:
> > Dear Anton,
> > 
> > Thanks for you help.
> > I got your two mails, but unfortunately I haven't managed to solve the
> > problem yet.
> > What exactly should I do in order to have the HO atom type when I run
> > grompp?
> > In fact I have used :
> > 
> > [phospho]$ pdb2gmx -f phosphoserine.pdb
> > 
> > choose the new option:  number 5
> >  0: Gromacs Forcefield (see manual)
> >  1: Gromacs Forcefield with all hydrogens (proteins only)
> >  2: GROMOS96 43a1 Forcefield (official distribution)
> >  3: GROMOS96 43b1 Vacuum Forcefield (official distribution)
> >  4: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
> >  5: ffG43a1 with SEP, TPO and PTR
> > 
> > and chose ffG43a1 with SEP, TPO and PTR for pdb2gmx,
> > 
> > Why should grompp not work when pdb2gmx was fine?  grompp is working with
> > the output of pdb2gmx! (.top)
> > 
> Because the rtp defines an atom that is not in the itp files of the
> force field. However, HO is a normal alcohol hydrogen that should be in
> there. Check the definitions of SEP etc. in your rtp file and compare
> them to the itp file. Do also look in your top file to see whether atom
> names have been translated appropriately into atomtypes. 
> 
> > thanks in advance
> > 
> > +-------------------------------------------------------------------------+
> > |                  Dra. Luciane Vieira de Mello Rigden                    |
> > | e-mail: mello at cenargen.embrapa.br                                       |
> > | Embrapa Recursos Geneticos e Biotecnologia                              |
> > | Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
> > | PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
> > | 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |
> > +-------------------------------------------------------------------------+
> > 
> > 
> > 
> > On Tue, 4 Feb 2003, Anton Feenstra wrote:
> > 
> > > Luciane Vieira de Mello wrote:
> > > [...]
> > > > I am not sure if I am checking the right file:
> > > > ffG43a1nb.itp
> > > > where I tried to add the HO atomtype from ffgmx2nb.itp, including the
> > > > pairtypes.
> > >
> > > There is also a .atp file (for Atom TyPes), but IIRC that is only
> > > used by pdb2gmx and not grompp... ;-(
> > >
> > >
> > > --
> > > Groetjes,
> > >
> > > Anton
> > >   ________ ___________________________________________________________
> > > |        | Anton Feenstra                                            |
> > > | .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> > > | |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
> > > | |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
> > > | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> > > |  /  \  |-----------------------------------------------------------|
> > > | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> > > |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
> > > |   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
> > > |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
> > > | (    ) |-----------------------------------------------------------|
> > > |  \__/  | "If You See Me Getting High, Knock Me Down"               |
> > > |        | (Red Hot Chili Peppers)                                   |
> > > |________|___________________________________________________________|
> > >
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-request at gromacs.org.
> > >
> > 
> > 
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> -- 
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> --__--__--
> 
> Message: 9
> From: Attila Borics <aborics at bif12.creighton.edu>
> To: gomacs <gmx-users at gromacs.org>
> Organization: 
> Date: 04 Feb 2003 15:18:37 -0600
> Subject: [gmx-users] D-Ala topology for OPLSAA
> Reply-To: gmx-users at gromacs.org
> 
> Hi!
> 
> I try to simulate a peptide containing D-Ala.
> I couldn't find this residue in OPLSAA's residue topology, 
> and since chirality is not defined by impropers as it is in GROMOS96,
> I'm a bit confused what should I use. Define an additional improper for
> the residue ALA, and insert it to .rtp as DALA, or try to manipulate
> with the dihedrals? If someone had this problem before please help me.
> Maybe someone already created a residue topology for D-Ala in OPLSAA.
> I would appreciate any help.
> Thanks
> 
> Attila 
-- 
Attila Borics <aborics at bif12.creighton.edu>



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