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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Received on Mon Aug 16 2010 - 05:00:03 PDT
