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

[Jordi Camps]

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?

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