Re: AMBER: query regarding loadpadb

From: Reena ..... <>
Date: Fri, 25 Apr 2008 16:37:21 +0530

Dear Anamika,

your job is perfectly fine. whenever u load a pdb file in leap it adds from
its side the missing H-atoms. if it says the unit is ok it means the
structure loaded is alrite....warning 22 are minor warnings...related to
some distances that are very close etc....these can be removed thru initial
minimisation or by relaxing the molecule in leap editor.
Rest depends on what kind of work u want to accordingly the
changes can be made in the pdb file...plz go through the amber tutorials for
more understanding


On Fri, Apr 25, 2008 at 2:03 PM, Anamika Awasthi <>

> Dear Amber,
> I just started to use AMBER. I am using serial version of AMBER 9.
> my protein is hexamer and having residues 1938
> I loaded my PDB file, it was showing total atoms in file 15126
> then it was showing "Leap added 15504 missing atoms according to residue
> templates"
> 6 Heavy
> 15498 H / lone pairs
> then I gave check command
> its showing warning 22
> unit is OK
> please, tell me if my job is proper or not and what I should analyze.
> Thanks in advance
> Anamika

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Received on Sun Apr 27 2008 - 06:07:52 PDT
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