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

[David]

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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