AMBER Archive (2004)

Subject: RE: AMBER: atoms not in residue templates

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Aug 04 2004 - 13:26:55 CDT

Dear Yongzhi

> > mol = loadpdb 1AVP.pdb
> Loading PDB file: ./1AVP_C.pdb
> Created a new atom named: H within residue: .R<NMET 1>
> Created a new atom named: HD1 within residue: .R<HIE
> 36>
> Created a new atom named: HD1 within residue: .R<HIE
> 54>
> Created a new atom named: HD1 within residue: .R<HIE
> 131>
> Created a new atom named: HD1 within residue: .R<HIE
> 143>
> Created a new atom named: HD1 within residue: .R<HIE
> 181>
> Created a new atom named: HD1 within residue: .R<HIE
> 188>
> Created a new atom named: HD1 within residue: .R<HIE
> 200>
> Created a new atom named: H within residue: .R<NGLY
> 205>
> total atoms in file: 2124
> Leap added 1275 missing atoms according to residue
> templates:
> 1275 H / lone pairs
> The file contained 9 atoms not in residue templates

All of your histidines are specified as HIS in your pdb file and so xleap
assumes that the protonation state of these residues is HIE (epsilon
nitrogen). However, your pdb file contains Hydrogen atoms in both the
epsilon and delta positions. For HIE there should be no HD1 proton. This is
what leap is complaining about. It found an HD1 proton for each of your
histidine residues when it wasn't expecting one. Since the HD1 protons don't
exist in the HIE residue map so they don't have types. The same is NMET and
NGLY, they have extra hydrogens present.

I would suggest that you go through your pdb carefully and specify the
protonation states of all your protonatable resiudes. If your histidines
really should be protonated on both nitrogens then you need to rename them
as HIP. Where did the protons come from btw? Is this structure a neutron or
NMR structure? If it is an x-ray structure then it is probably best to
remove all the protons from the file and have xleap add them for you
automatically. Just be sure to know how many you expect to be added for the
protonation state you think your protein is in and ensure xleap add the
right number.

I hope this helps.
All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

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