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

Jordi Camps jcamps at lsi.upc.edu
Mon May 2 11:28:35 CEST 2005

Hi all!

Paste back the coordinates of my original file is my next step, but because
of the change in atom name AND number I must compare the original
coordinates and the new coordinates and select the closest one for
substitution. Which method do you think that will be more precise? Minimal
difference? Minimal root mean squared?

This cold be avoided if someone can ensure that pdb2gmx ALWAYS change O->O2
and OXT->O1. Then I could select the atoms by name, which is easier and we
won't be guessing.

Thanks for your help :-)

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 Anton Feenstra
Enviado el: lunes, 02 de mayo de 2005 9:52
Para: Discussion list for GROMACS users
Asunto: Re: [gmx-users] RE: Converting from AMBER to GROMACS

Jordi Camps wrote:

> Hello,
> In the process of conversion I've been making a lot of advances. Right 
> now I think that I only have one thing to solve. When I feed my .gro 
> file to the pdb2gmx in order to generate the topology, it complains 
> about a repeated oxygen and deletes it. This oxygen is terminal, and 
> the same pdb2gmx adds another one in slightly different coordinates. 
> If I reprocess the output
> (conf.gro) with the same program, the same problem occurs.
> Is there any way to get the pdb2gmx understand which is the terminal 
> oxygen and not rewrite another one?

Not that I know of. The first step, deleting the oxygen, is part of the 
initial consistency check of your input file. At this stage, it is hard 
to make pdb2gmx already aware of a possible carbonyl group at the terminus.

You can always paste back in the coordinates from your input file, into 
the pdb2gmx output file...



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  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
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