AMBER Archive (2002)

Subject: Re: structure

From: David Case (case_at_scripps.edu)
Date: Wed Jul 31 2002 - 00:43:50 CDT

On Tue, Jul 30, 2002, Cozmuta wrote:
>
> I am trying to generate the prmtop and inpcrd files for a protein. Leap is
> adding hydrogens to it (althought the pdb structure was already edited in
> InsightII and hydrogens were added there according to the experimental
> pH). But then when I want to save the .prmtop and .inpcrd files I get the
> following error message for all those Hydrogens added by Leap.
>
> FATAL: Atom .R<MET 2049>.A<HG1 19> does not have a type.
>

The names of all atoms in the input pdb file must match those in the Amber
libraries; this includes hydrogen atoms.

I really suspect that the above example is not a "hydrogen added by LEaP",
but rather a hydrogen present in your input pdb file that does not match
the names Amber expects.

Because of its NMR origins, the Amber libraries use IUPAC names for protons;
these differ from names used by Brookhaven. For example, the CG carbon
in MET has protons HG1 and HG2 in Brookhaven (and I assume, Insight),
whereas those protons are HG2 and HG3 in the IUPAC nomenclature. Hence,
LEaP found HG1 in the input file and didn't know what to do with it.

There are several things you can do:

1. remove protons from your input pdb file, and let LEaP rebuild them.

2. If you really want to keep the original proton positions, use protonate
with the -k option to rename everything according to the Amber conventions.

3. Rewrite the libraries in $AMBERHOME/dat/leap/lib to use the naming
convention you want. (Not as hard as it might sound).

...hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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