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

[James Lord]

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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.