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

Jordi Camps jcamps at lsi.upc.edu
Tue Apr 19 12:37:28 CEST 2005

Hi Erik!

This is my objective: get a .gro file.
But I can't start from a .gro file. My input is from AMBER. I have the
topology (prmtop) and a restart file (protein.md_0.r) in AMBER format (other
AMBER files are available, like the original PDB, but I think that they are
irrelevant). With "ambpdb" I can get a PDB file with the coordinates
corresponding to the last step of the restart file. I don't know any way to
get a .gro file with this inputs, so I'm trying to do it myself.

The objective is to continue the simulation in the restart point, in order
to compare the trajectories obtained with AMBER and GROMACS. So I can't get
the original PDB, solvate, ionizate, equilibrate, minimizate and, at least,
simulate, because the starting points won't be the same.

Maybe I'm missing some AMBER utility that can do this conversion :-/

Thank you very much,

Jordi Camps Puchades
Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
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 Erik Lindahl
Enviado el: lunes, 18 de abril de 2005 19:00
Para: Discussion list for GROMACS users
Asunto: Re: [gmx-users] RE: Converting from AMBER to GROMACS

Hi Jordi,

The easiest solution is to use a format like .gro, which in contrast to 
.pdb contains velocities.

Although the tool is called "pdb2gmx", it can read all coordinate files 
just like the other gromacs programs, so if you just start from a .gro 
file (with velocities) it should be able to maintain them, and just 
create a reordered topology and new gro file for you.



On Apr 18, 2005, at 6:47 PM, 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?
> Thank you!
> --
>> -----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,

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