[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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