Dear Dr. case,
Thank you.
Regards,
kamlesh
On Mon, Aug 16, 2010 at 8:41 PM, case <case.biomaps.rutgers.edu> wrote:
> On Mon, Aug 16, 2010, kamlesh sahu wrote:
> > The file "protonate-com.out" contains these lines -
> >
> > Here are the mystery protons from input file:
> >
> > HD1 HIE 973 -6.92 8.32 35.72
>
> An "HIE" residue should not have an "HD1" proton, so the program is telling
> you it doesn't know what to do with it.
>
> > HG CYS1168 -43.37 -0.32 57.45
>
> This is more complex: the program built an HG atom, but it was not at the
> same
> place as the one that was there (which is OK). Use the -k option if you
> wish
> to keep the proton positions in the initial file.
>
> > HAV DXQ2000 -41.51 14.55 48.53
>
> Protonate only works with proteins. Since you already seem to have protons
> on your DXQ ligand, you probably don't need to send this ligand through
> protonate.
>
> >
> > Further I wish to use
> > 2. ambpdb -pqr -p complex.prmtop < complex.inpcrd > complex.pqr
> > 3. pol_h < complex.pqr > complex-1.pdb
> > Will I need to specify frcmod file for DXQ in pol_h command ?
>
> These commands don't make much sense. To make a prmtop file, you already
> need
> t know the positions of all the hydrogens. In that case, you don't need to
> run pol_h.
>
> Neither protonate nor pol_h are generally needed if you just wish to
> prepare a
> system for MD simultion. You may want to think carefully about why you are
> running these codes. Furthermore, the "reduce" program is probably a
> better
> choice nowadays for adding hydrogen atoms to structures that lack them.
>
> ....dac
>
>
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>
--
Kamlesh Kumar Sahu (post doc researcher)
Riken, wako, Saitama, JAPAN
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Received on Mon Aug 16 2010 - 08:30:04 PDT
