[gmx-users] RE: Converting from AMBER to GROMACS
David van der Spoel
spoel at xray.bmc.uu.se
Tue Apr 19 08:50:37 CEST 2005
On Tue, 2005-04-19 at 01:21 +0200, Jordi Camps wrote:
> Hello!
>
> Pdb2gmx outputs an optional index file, but its contents are of the form:
> [xxxxxx]
> 1 2 3 4 5 6 .. 20000
>
> And it not serve my purpose. Also I wnt to conserve the hydrogens (I don't
> want to use the -ignh option), but the program said me that:
> Fatal error: Atom HA in residue SER 1 not found in rtp entry with 8
> atoms
> while sorting atoms. Maybe different protonation state.
Maybe you chose the wrong force field? Use OPLS for all-atom
simulations. You will have to rename 2HB to HB1 and 3HB to HB2 etc. We
try to adhere to IUPAB standard for protein nomenclature. Unfortunately
there are at least four common naming schemes for hydrogens out there
which makes life difficult for a programmer..
> Remove this hydrogen or choose a different protonation state.
> Option -ignh will ignore all hydrogens in the input.
> And I'm not sure where I can check the names. The beginning of my pdb input
> file is:
> REMARK
> ATOM 1 N SER 1 29.323 53.812 32.927
> ATOM 2 H1 SER 1 29.325 54.503 33.664
> ATOM 3 H2 SER 1 29.909 54.077 32.149
> ATOM 4 H3 SER 1 29.854 53.021 33.263
> ATOM 5 CA SER 1 27.984 53.380 32.550
> ATOM 6 HA SER 1 27.347 53.185 33.413
> ATOM 7 CB SER 1 27.275 54.523 31.757
> ATOM 8 2HB SER 1 27.677 54.572 30.745
> ATOM 9 3HB SER 1 26.197 54.377 31.688
> ATOM 10 OG SER 1 27.454 55.694 32.461
> ATOM 11 HG SER 1 26.913 56.387 32.076
> ATOM 12 C SER 1 28.136 52.199 31.614
> ATOM 13 O SER 1 28.670 52.289 30.515
> ATOM 14 N TRP 2 27.661 51.058 32.011
> ATOM 15 H TRP 2 27.372 51.081 32.979
>
> How should I modify the hydrogen names (or the config files) to get que .top
> and .gro files correctly generated?
>
> Thank you!
>
> --
> Jordi Camps Puchades
> Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
> UPC-CIRI
> c/. Jordi Girona 1-3
> Modul C6-E201 Tel. : 934 011 650
> E-08034 Barcelona Fax : 934 017 014
> Catalunya (Spain) e-mail: jcamps at lsi.upc.edu
>
> -----Mensaje original-----
> De: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] En
> nombre de David
> Enviado el: lunes, 18 de abril de 2005 19:03
> Para: Discussion list for GROMACS users
> Asunto: Re: [gmx-users] RE: Converting from AMBER to GROMACS
>
>
> On Mon, 2005-04-18 at 18:47 +0200, Jordi Camps wrote:
> > Information update:
> >
> > The "Long Bond" warnings exists due to the way I changed some names
> > in the PDB file. It is not a "pdb2gmx" problem nor a PDB problem. It
> > was my fault. But the question is there: how can I get a correlation
> > betweeb the old restart file and the new PDB?
> I think pdb2gmx also outputs an optional index file which can be used for
> renumbering
> >
> > Thank you!
> >
> > --
> >
> > Jordi Camps Puchades
> >
> > Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
> > UPC-CIRI c/. Jordi Girona 1-3
> > Modul C6-E201 Tel. : 934 011 650
> > E-08034 Barcelona Fax : 934 017 014
> > Catalunya (Spain) e-mail: jcamps at lsi.upc.edu
> >
> > > -----Mensaje original-----
> > > De: Jordi Camps [mailto:jcamps at lsi.upc.edu]
> > > Enviado el: lunes, 18 de abril de 2005 18:31
> > > Para: 'gmx-users at gromacs.org'
> > > Asunto: Converting from AMBER to GROMACS
> > >
> > > Hello everybody!
> > >
> > > I'm trying to convert an AMBER restart file to a GROMACS
> > > input in order to continue the simulation on GROMACS. The
> > > approach that I choose has been to generate a PDB from the
> > > restart file with "ambpdb", change some names in the
> > > resulting PDB to make "pdb2gmx" happy and then run "pdb2gmx"
> > > in order to get the topology file and the .gro file. Then I
> > > want to add the velocities to the .gro file generated from
> > > the AMBER restart file.
> > >
> > > Just now I have one problem and a doubt:
> > > -Problem: when I run "gmx2pdb", I get about 18 messages
> > > like "Warning: Long Bond (94-96 = 4.82075 nm)", and this is not good.
> > > -Question: in order to add the velocities to the .gro
> > > file from the AMBER restart file, I need the atoms to
> > > maintain the same numeration, but I think that "gmx2pdb"
> > > changes the numeration (reorders the atoms without conserving
> > > the numbers). Is there some way I can accomplish this?
> > >
> > > Thank you very much in advance,
> > >
> > > --
> > >
> > > Jordi Camps Puchades
> > >
> > > Instituto Nacional de Bioinformatica (INB) Nodo Computacional
> > > GNHC-2 UPC-CIRI c/. Jordi Girona 1-3
> > > Modul C6-E201 Tel. : 934 011 650
> > > E-08034 Barcelona Fax : 934 017 014
> > > Catalunya (Spain) e-mail: jcamps at lsi.upc.edu
> >
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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
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