On Fri, Sep 27, 2013 at 9:10 AM, Concha, Monica
<Monica.Concha.ars.usda.gov>wrote:
> Hello Shomesankar Bhunia,
>
> Please how did you fix it?
>
HD1 is a proton on the delta-Nitrogen of the Histidine. HIE is the
epsilon-protonated residue (HIS is interpreted as HIE by tleap). HID is
the delta-protonated residue. HIP is the double-protonated histidine
residue.
If you know the Histidine is protonated in the delta position, change the
residue name of that histidine to HID in the PDB file. (Or HIP if it is
doubly-protonated).
You can also get rid of all Hydrogen atoms (reduce -Trim your.pdb >
your_noh.pdb) and let tleap add hydrogens for you (although if you want the
proton on the delta position, as you might, you have to change the residue
name in the PDB as described above).
Good luck,
Jason
>
> 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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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 27 2013 - 09:30:02 PDT
