Dr. Case:
Thank you very much for your reply. It sounds easier to just let LEaP
add the protons--but what command in LEaP does this? I couldn't find a
command that added protons. Also, will LEaP be confused by the fact
that it is an abnormal residue? I am in something of a circular
predicament in that I need to know the coordinates of the added
protons so that I can run the file through GAMESS to find the
electrostatic point charges so that I can write a library file to make
this residue readable by AMBER. Please let me know any suggestions
that you have.
Thank you again for your help.
Kenley
On Apr 8, 2005 10:49 AM, David A. Case <case.scripps.edu> wrote:
> On Thu, Apr 07, 2005, Kenley Barrett wrote:
>
> > I am having some difficulties with the protonate command. I have an
> > "abnormal" residue in my protein: a methylated histidine. For some
> > reason with this residue (and not with any of the normal residues) the
> > protonate command leads to the placement of atoms that are named with
> > a "?"
>
> Protonate only knows about ordinary amino acids. If you have a chemical
> modification, you will have to modify the PROTON_INFO file (which, as you
> will see, is where the "?" are coming from.)
>
> [The "HIC" residue in PROTON_INFO is for a histidine bound to copper, not for
> methylated histidine.]
>
> But, are you sure you need protonate at all? In most cases, just letting LEaP
> add in missing protons is sufficient.
>
> ...good luck....dac
>
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Received on Mon Apr 11 2005 - 22:53:00 PDT
