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 Thu May 05 2005 - 23:53:00 PDT
