AMBER Archive (2009)

Subject: RE: [AMBER] Error in xleap

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jan 15 2009 - 10:01:20 CST

Hi Archana,

> I am using xleap of amber10. When i provide the command
> saveamberparm f1 1prb.top 1prb.crd
>
> I get the following error:
> Checking unit
> FATAL: Atom .R<HIE 52> .A<HD1 18> does not have a type.
> Failed to generate parameters.
> Parameter file was not saved.

This is because Epsilon protonate histidine has no HD1 atom but there is one
in your pdb file. Do you know the origin of these hydrogens? How were they
determined as part of the structure determination? Is this a NMR structure
rather than a xray one?

Take a look at this residue and see which of the two nitrogens in the
histidine are protonated. If they are both protonated you should rename the
residue HIP, if it is just the delta N protonated name it HID, if it is just
the epsilon N protonated name it HIE.

Good luck,
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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