[gmx-users] PDB2GMX warnings

Xavier Periole x.periole at chem.rug.nl
Mon Feb 16 19:48:01 CET 2004

davide.demiliano at fastwebnet.it wrote:

>I've just started using GROMACS software for the first time to simulate
>a small lipid bilayer. When I try to create my .gro file using pdb2gmx a
>get several long bond warnings! What dose it mean exactly? (a ectually get
>my .gro file at the end of the process and the .pdb file I use it's already
>been used for other simulations). Thanks for your help
>Dr Davide D'Emiliano
>phd student
>Physics department
>Universita' degli studi di Roma "La Sapienza"
>Rome, Italy
>gmx-users mailing list
>gmx-users at gromacs.org
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I don't know about the new pdb2gmx, but the old version does not
support the lipid bilayers ...

You can use the editconf to generate .gro, you can also use the .pdb
just be sure that the atom types are correct (As in lipid.itp).



   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: md.chem.rug.nl/~periole

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