[gmx-users] Re: gmx-users Digest, Vol 30, Issue 18

[Miguel Ortiz Lombardia]

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Hi, Stefan,

To the first question: (run in Ubuntu)

> locate cpp | grep "/cpp$"
/lib/cpp
/usr/bin/cpp
/usr/share/doc/cpp

For the second, you must make sure that the atom names, for example,
from your Prodrg topology are compatible with those in the force field
you are using. Prodrg generates AMBER topologies, IRIC.

Cheers,



Miguel

Stefan Schöbel wrote:
> Hi folks,
> 
> I am running Gromacs under Linux Ubuntu. My question: where is my cpp located? It is not under /usr/bin/cpp.
> And the other question: I try to simulate a protease together with its lipopeptide inhibitor, so I used Prodrg to get the files of the inhibitor but I get warnings that some atom types are not known, for example "HO".
> How do I know which are the correct atom type descriptions?
> I guess these are the typical beginner questions, so I hope someone knows the answers. :)
> 
> 
> Bye Stefan

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: molatwork at yahoo.es
www: http://www.ysbl.york.ac.uk/~mol/
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Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie.                          (Raoul Vaneigem)
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