I just removed all the hydrogen atoms from the pdb file (ligand and
protein) and let leap add all the hydrogens. As you can find the problem "
FATAL: Atom .R<HIE 57>.A<HD1 18> does not have a type." is due to hydrogen
atom.Hope it helps.
On Fri, Sep 27, 2013 at 6:40 PM, Concha, Monica
<Monica.Concha.ars.usda.gov>wrote:
> Hello Shomesankar Bhunia,
>
> Please how did you fix it?
>
> Monica C. Concha
> Physical Science Technician
> Cotton Structure and Quality Research
> Southern Regional Research Center
> 1100 Robert E. Lee Blvd.
> New Orleans, LA 70124
> monica.concha.ars.usda.gov
>
>
> phone: 504-286-4252
> -----Original Message-----
> From: Shomesankar Bhunia [mailto:rightclickatrighttime.gmail.com]
> Sent: Friday, September 27, 2013 5:10 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] histidine_residue
>
> I solved the problem from a previous amber post.
>
>
> On Fri, Sep 27, 2013 at 2:54 PM, Shomesankar Bhunia <
> rightclickatrighttime.gmail.com> wrote:
>
> > Dear all,
> > I am getting a error in leap while loading my *.pdb file.
> > How to resolve it? Thanks in advance
> >
> >
> >
> >
> > complex = loadpdb Imidazole_docked_prlig.pdb Loading PDB file:
> > ./Imidazole_docked_prlig.pdb Created a new atom named: HD1 within
> > residue: .R<HIE 57> Created a new atom named: HD1 within residue:
> > .R<HIE 84> Created a new atom named: HD1 within residue: .R<HIE 92>
> > Created a new atom named: HD1 within residue: .R<HIE 149> Created a
> > new atom named: HD1 within residue: .R<HIE 204>
> > total atoms in file: 3716
> > Leap added 13 missing atoms according to residue templates:
> > 13 H / lone pairs
> > The file contained 5 atoms not in residue templates
> > > saveamberparm complex asd.prmtop asd.inpcrd
> > Checking Unit.
> > WARNING: The unperturbed charge of the unit: 2.001000 is not zero.
> > FATAL: Atom .R<HIE 57>.A<HD1 18> does not have a type.
> > FATAL: Atom .R<HIE 84>.A<HD1 18> does not have a type.
> > FATAL: Atom .R<HIE 92>.A<HD1 18> does not have a type.
> > FATAL: Atom .R<HIE 149>.A<HD1 18> does not have a type.
> > FATAL: Atom .R<HIE 204>.A<HD1 18> does not have a type.
> > Failed to generate parameters
> > Parameter file was not saved.
> >
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Received on Fri Sep 27 2013 - 09:00:03 PDT
