Try the following awk command to remove hydrogens
awk '($3 !~ /^[123]?H/ ){print}' pdbinputfile > pdbfile_nohydrogens
On Thu, 2005-05-05 at 23:02, Thomas Patko wrote:
> AMBER Users:
>
> After looking at the input PDB with a graphical viewer
> (PCModel9) it seems that the problem may be related to
> stray or misplaced protons in the PDB. I have not been
> able to find the command to strip all protons from my
> original PDB. There are also missing parameters when
> trying to do a minimization in PCModel on this original
> PDB using the built-in AMBER forcefield (segmentation
> faults results). I know that I can reprotonate with the
> command line protonate program once I have stripped the
> erroneous or stray protons out.
>
> Any helps would be appreciated.
>
> Regards,
>
> Thomas Patko
>
> Graduate Student
> Department of Chemistry & Biochemistry
> California State University, Long Beach
> Dr. Marco Lopez Research Group
>
> On Wed, 04 May 2005 10:13:35 -0700
> "Thomas Patko" <tpatko.csulb.edu> wrote:
> > AMBER Users:
> >
> > I am trying to load the very small protein bromelain to
> >do some MD simulations. There seems to be a problem with
> >the connectivity between each residue when I load it in
> >xleap. Am I doing something wrong here or is there a
> >problem with the initial PDB file? The protein of
> >interest is attached to this e-mail as is my output from
> >xleap (leap.log) when I try to load the protein in xleap.
> >
> > Regards,
> >
> > Thomas Patko
> >
> > --
> > Graduate Student
> > Department of Chemistry & Biochemistry
> > California State University, Long Beach
> > Dr. Marco Lopez Research Group
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Received on Fri May 06 2005 - 12:53:00 PDT
