Re: [AMBER] protonate

From: case <case.biomaps.rutgers.edu>
Date: Mon, 16 Aug 2010 07:41:15 -0400

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
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