AMBER Archive (2008)

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

From: Steve Spronk (spronk_at_umich.edu)
Date: Mon Apr 21 2008 - 12:04:34 CDT

Hi Cristina,

Just a note that you should take a moment to consider the protonation states
of your histidine residues. As you know, HIS has three different states:
two neutral forms with the proton on the NE or ND, and one charged form with
protons on both. Specific protonation states of HIS residues can be
specified by naming the residues HID (proton on ND), HIE (proton on NE), or
HIP (proton on both). Note that when tleap encounters a residue named HIS,
it equates it with HIE.

You have a PDB file that contains protons, and three of the HIS residues in
the file have HD1 atoms. Assuming that these residues were named HIS, tleap
treated them as HIE residues, which do *not* have HD1 atoms; this was the
reason for the warning messages about creating new atoms. (You can confirm
that it thinks they're HIE residues because the warning messages report them
as HIE 3, HIE 86, and HIE 100.) I also can assume that your PDB file *did*
have HE2 atoms, because there was no complaint from tleap about missing HE2
atoms. Therefore, these three residues exist as cationic residues in your
PDB file.

When you erased the hydrogens from the PDB files and re-read the PDB into
tleap, everything worked fine because it added its own protons in places
wherever it thought they should go. However, if you kept the residues names
as HIS and did not change them to HIP, the HD1 atoms were not added to the
side chains, and therefore you do not have positively-charged His residues
in your MD system.

I have no idea what system you're working on, so it may be perfectly fine
that these residues are uncharged instead of charged. But given that the
PDB file had them in the charged form, you should figure out if it makes
sense to keep them charged in the MD.

Steve

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Cristina Sisu
> Sent: Tuesday, April 15, 2008 10:50 AM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: loading pdb in leap to create parameter files
>
> 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
> >>
> >
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu