AMBER Archive (2008)

Subject: Re: AMBER: loading pdb in leap to create parameter files

From: Cristina Sisu (csds2_at_cam.ac.uk)
Date: Tue Apr 15 2008 - 09:50:12 CDT

Thanks a lot!
It worked!

Da-Wei Li wrote:
> The most easy way is to remove the H atoms in the PDB file and let
> leap add them.
>
> On Tue, Apr 15, 2008 at 9:43 AM, Cristina Sisu <csds2_at_cam.ac.uk> wrote:
>
>> Dear AMBERs,
>>
>> I am new in working with Amber. I am using Amber 9, and I got stuck
>> quite at the beginning of creating the parameter files .prmtop and
>> .inpcrd. The story is like this:
>> I've downloaded a pdb from the protein databank (NMR sturcture).
>> I've edited the file to save only one model for the protein. I've loaded
>> the file into leap for creating the parameter files. When I load it, it
>> automatically ads H atoms to the 3 HIS residues, on the N, charging
>> therefore my molecule. However at the end of this process I get the
>> following massage:
>> """
>> > Created a new atom named: HD1 within residue: .R<HIE 3>
>> > Created a new atom named: HD1 within residue: .R<HIE 86>
>> > Created a new atom named: HD1 within residue: .R<HIE 100>
>> > total atoms in file: 2069
>> > Leap added 3 missing atoms according to residue templates:
>> > 3 H / lone pairs
>> > The file contained 3 atoms not in residue templates
>> > Since added/missing = extra, there is a high probability
>> > of atoms with 'incorrect' names; you may want to
>> > use addPdbAtomMap to map these names, or change in file
>> """
>> First time, I've ignored their warning and I tried to go on saving my
>> parameter files. However I got the error:
>> """
>> > FATAL: Atom .R<HIE 3>.A<HD1 18> does not have a type.
>> > FATAL: Atom .R<HIE 86>.A<HD1 18> does not have a type.
>> > FATAL: Atom .R<HIE 100>.A<HD1 18> does not have a type.
>> > Failed to generate parameters
>> > Parameter file was not saved.
>> """
>>
>> I've tried then to use the AddPdbAtomMap option trying to indicate that
>> I want the HD1 atoms to be regarded as HE2 (already in the HIS map file,
>> Hydrogen atoms)
>>
>> > addPdbAtomMap {{HE2 HD1}}
>>
>> Then I've looked at the description for His in the aminoacid database of
>> Amber. It has only 17 described atoms, and obviously the new H on the N
>> is not present.
>> I've looked for an answer in the manual, on the FAQ and in the mail
>> archive, but I found no answer. Can you please help me figure out how
>> - to define the type of the new atom create?
>> or
>> - to make Amber do not add H on my protein?
>> or
>> - anyother way to solve this problem?
>>
>>
>> Thanks,
>>
>> Cristina
>>
>

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