[gmx-users] RE: Converting from AMBER to GROMACS
lindahl at sbc.su.se
Mon Apr 18 19:00:04 CEST 2005
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
> old restart file and the new PDB?
> Thank you!
> 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: 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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