[gmx-users] modelling/adding missing residues in case of Fatal error: Incomplete ring in HIS3

[范聪]

Hello, as to this situation, what I often do is to open the pdb file with editing software such as schrodinger or SYBYL, then "mutate" the incomplete residue to a complete one. Also, in these software, there will be a "protein preparation wizard" to help you check and repair the protein structure.
At 2015-05-09 15:13:40, James Lord <jjamesgreen110 at gmail.com> wrote:
>Hi Justin,
>I opened up the strucutre in Swissviewr. Then how can I have a pdb with
>missing parts added?
>Cheers
>James
>
>On Tuesday, May 5, 2015, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 5/5/15 4:32 AM, James Lord wrote:
>>
>>> Dear gmx users,
>>>
>>> pdb2gmx is complaining about Incomplete ring in HIS3, for 3V03.pdb
>>>
>>> I saw Justin's comment
>>> "All structures have to be complete in order for pdb2gmx to process them.
>>> The only atoms it can add are hydrogens. All heavy atoms are required. If
>>> you place the missing atom(s) correctly, according to proper geometry,
>>> you shouldn't
>>> be changing the structure too much, but a simple energy minimization after
>>> you've generated the topology should relax any poor geometry.
>>>
>>> Justin"
>>>
>>> And also Florian comment on this
>>>
>>> "you should take a look at the structure in your favorite viewer,
>>> perhaps some residues are missing and/ or
>>> are not resolved completly by Xray/ NMR. Take a look
>>> at REMARKS in this pdb file.
>>>
>>> Programs for modelling missing residues are:
>>>
>>> Swiss
>>>
>>> pdb
>>> viewer
>>>
>>> WHATIF
>>>
>>> pymol
>>>
>>> vmd
>>>
>>> or
>>>
>>> commercial
>>> onces:
>>>
>>> MOE
>>>
>>> Accelyrs
>>>
>>> Discovery
>>> Studio"
>>>
>>> I  see following remarks in the .pdb
>>>
>>> REMARK
>>> 465 MISSING RESIDUES
>>>
>>
>> Missing residues are important if they are internal or otherwise important
>> for function.  Frequently, terminal residues are disordered and cannot be
>> resolved by crystallography.
>>
>>  REMARK
>>> 470 MISSING ATOM
>>>
>>>
>>> REMARK
>>> 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
>>>
>>>
>> Here's the most important section of your PDB file (at least, in this
>> context):
>>
>> REMARK 470 MISSING ATOM
>> REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
>> REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
>> REMARK 470 I=INSERTION CODE):
>> REMARK 470   M RES CSSEQI  ATOMS
>> REMARK 470     HIS A   3    CG   ND1  CD2  CE1  NE2
>> REMARK 470     LYS A   4    CE   NZ
>> REMARK 470     LYS A  41    CD   CE   NZ
>> REMARK 470     LYS A  76    CE   NZ
>> ...
>>
>> You have hundreds and hundreds of missing atoms in this structure.  They
>> need to be modeled back or there will be no way to produce a topology.
>>
>>
>>> REMARK
>>> 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
>>>
>>>
>>> REMARK
>>> 470 I=INSERTION CODE):
>>>
>>> 1-I also looked at the structure in VMD but how can I see the
>>> missingatoms/residues?How to know what type of atom/residues are
>>> missing? I just can see residue number
>>>
>>>
>> Read the contents of the PDB file, i.e. the snippet that I posted.
>>
>>  2- How to add them? Again somewhere else Justin is saying “add the missing
>>> atoms with emacs (or another text editor). Then minimize” .
>>>
>>>
>> This certainly doesn't apply to you.  If you're missing an atom or two,
>> it's trivial to calculate where they should be based on existing atoms.  In
>> your case, you have a huge amount of missing atoms.  Try SwissPDBViewer
>> (which adds back missing atoms as soon as you open the file - convenient!)
>> or anything else you might like (I think WHATIF can do this, too, but I've
>> never done it).
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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