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

[James Lord]

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


REMARK
465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE


REMARK
465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN


REMARK
465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)

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):

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

2- How to add them? Again somewhere else Justin is saying “add the missing
atoms with emacs (or another text editor). Then minimize” .

May I ask someone to walk me through these steps?

Cheers

James