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

[Justin Lemkul]

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

==================================================