[gmx-users] pdb2gmx error H atoms not found in rtb Database

David van der Spoel spoel at xray.bmc.uu.se
Wed May 19 08:54:50 CEST 2004

On Wed, 2004-05-19 at 05:06, p.keymer at student.qut.edu.au wrote:
> Hi All
> This is my first time using Gromacs.  I have been trying to
> gonerate a topology for a few protiens however every time I
> run pdd2gmx I encounter this (or a similar) fatal eror.
> Fatal error: Atom HB1 in residue ARG 1 not found in rtp
> database while sorting atoms. Maybe different protonation
> state. Remove this hydrogen or choose a different protonation
> state. Option -ignh will ignore all hydrogens in the input.
> I have managed to overcome this problem by editing the pdb
> file and removing the H atoms as the output sugests. However i
> am concerned that this will affect the results.
> Please can someome help me 
> Have I Done the right thing or is there another way to do
> this?

It would have been easier to add the -ignh flag. But what matters is
which force field you use. The OPLS force field does have all atoms
while the gromos force fields do not. This does *not* imply
automatically that OPLS is better.
> Thank you 
> Philip
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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