[gmx-users] pdbgmx warning long bond

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Jan 26 09:52:08 CET 2007

Hi Maite,

The thing is, if pdb2gmx does not encounter a TER statement or chain
identifier, it usually tries to bind everything it finds together
consecutively. So, you could try to add a number of TER statements,
but still, it is better to generate the topology for your protein
separately by running it through pdb2gmx and then adding the things
together. That will also make your topology much smaller.


On 1/25/07, maite lopez <lopezmai at gmail.com> wrote:
> Hi Tsjerk:
> But, i think the problems is that pdb2gmx program  see the membrane
> how a protein and it tries to tie the peptide with the membrane. The
> topology of dppc membrane appear in the ffG53a5.rtp file of gromacs.
> What can i do? Should  i create a peptide.top file and include it a
> lipid.itp and dppc.itp file?
> The lipid.itp file i took from Dr. Peter tieleman site is for GROMOS87
> forcefield and i use GROMOS96 forcefield.
> Thanks for the help,
> Maite
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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