[gmx-users] Converting from AMBER to GROMACS

[Jordi Camps]

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