[gmx-users] pdb2gmx does create bonds b/w DNA bases!

[Anton Feenstra]

Azazel S'irim wrote:
> Hi,
> 
> I'm trying to do MD on a dsDNA dodecamer.  After
> spending two days on this, I finally figured out why
> grompp crashes.  It appears that pdb2gmx does not
> create the bond between the individual DNA
> nucleotides.  There is no bond connecting the O3' of
> the n-1 residue with the P of residue n.  And because
> of this no dihedral values are written for the
> corresponding dihedral angle and that makes pdb2gmx
> crash.  Any suggestions!?  Where is the info for
> 'linking' residues contained?  I'm using GROMOS96
> (official distribution) forcefield.  Thanks

These bonds come from the descriptions in the .rtp file (e.g. ffG43a1.rtp)
where bonds (and angles and dihedrals) are defined with atoms like '-P',
or '+O' for bonds to the previous, or next residues respectibely (it could \
be defined either way in the file, I don't know right now...).

So, check your .rtp file. pdb2gmx will print exactly which one it is using
(like 'opening library file /some/dir/gromacs/share/top/ffG43a1.rtp')


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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