AMBER Archive (2009)

Subject: RE: [AMBER] NATOM in prmtop and inpcrd files does not agree with the input

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Aug 24 2009 - 23:55:52 CDT

Hi Maria,

> I am trying to debug some errors during sander runs. One thing that I
> am
> noticing is that both my crd and prmtop files have NATOM which do not
> agree
> with the input at all.
> The actual pdb has 1994 atoms, leap adds 2 missing heavy atoms. yet
> both the
> prmtop and crd files somehow have 4012 atoms listed.
>
> > rec = loadpdb 1BVR_protonly.pdb
> Loading PDB file: ./1BVR_protonly.pdb
> Added missing heavy atom: .R<NTHR 2>.A<CG2 9>
> Added missing heavy atom: .R<NTHR 2>.A<OG1 13>
> total atoms in file: 1994
> Leap added 2018 missing atoms according to residue templates:
> 2 Heavy
> 2016 H / lone pairs
> > saveamberparm rec rec.prmtop rec.inpcrd

elided....
 
> in the crd file. Is this an error, and if so, any ideas why this is
> occuring? (I have tried this with multiple pdb files for the same
> target, to
> no avail.)

Looks fine to me. Your pdb file has 1994 atoms. It appears to be missing two
of the N terminal heavy atoms so leap added these for you based on the
internal coordinate templates. Since most pdb files do not contain any
hydrogens, since hydrogens do not defract x-rays enough to be seen in most
crystal structures since they only have 1 electron. Leap thus added 2016
hydrogen atoms to your system based on the default protonation states. This
means Leap added a total of 2018 atoms to the already defined 1994 atoms.
Summing these two values gives the 4012 atoms that you observe in the prmtop
and inpcrd files.

If you run this prmtop and inpcrd file through ambpdb you can generate
yourself a pdb file which will contain all the of the hydrogens and missing
heavy atoms.

Note, if you are not planning on running with implicit solvent here then you
should also solvate your system which will add more atoms.

All the best
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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