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 - 06:30:03 PDT
