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

Erik Lindahl lindahl at sbc.su.se
Tue Apr 19 12:59:27 CEST 2005


Right, but both the .pdb and .gro formats are almost trivial. You can 
easily write a perl tool to convert between them.

My point was just that the main use of pdb2gmx is to create the Gromacs 
*topology* from some coordinates, and these coordinates can be a .gro 
file with velocities if you want to avoid entering them yourself after 
starting from a pdb file. This way pdb2gmx will take care of all the 
reordering for you.



On Apr 19, 2005, at 12:37 PM, Jordi Camps wrote:

> 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.
> Cheers,
> Erik
> 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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