[gmx-users] modelling/adding missing residues in case of Fatal error: Incomplete ring in HIS3
jjamesgreen110 at gmail.com
Tue May 5 10:32:12 CEST 2015
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,
be changing the structure too much, but a simple energy minimization after
you've generated the topology should relax any poor geometry.
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:
I see following remarks in the .pdb
465 MISSING RESIDUES
465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
470 MISSING ATOM
470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
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?
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