[gmx-users] RE: Converting from AMBER to GROMACS

Tue Apr 19 01:21:53 CEST 2005

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.
      	       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
> 
> _______________________________________________
> 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.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

_______________________________________________
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.