[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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