[gmx-users] Angles not read

Steven Neumann s.neumann08 at gmail.com
Mon Jun 10 14:23:09 CEST 2013

Dear Gmx Users,

I created my own CG force field and i process my structure to pdb2gmx. I
process 3 beads I created to check whether the topology is properly created:

Using the CG force field in directory ./CG.ff

No file 'watermodels.dat' found, will not include a water model
Reading 60central_Carbons.pdb...
Read 3 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 3 residues with 3 atoms

  chain  #res #atoms
  1 'X'     3      3

All occupancy fields zero. This is probably not an X-Ray structure
Opening force field file ./CG.ff/atomtypes.atp
Atomtype 1
Reading residue database... (CG)
Opening force field file ./CG.ff/aminoacids.rtp
Reading .rtp file without '[ bondedtypes ]' directive,
Will proceed as if the entry

[ bondedtypes ]
; bonds  angles  dihedrals  impropers all_dihedrals nr_exclusions HH14
     1       1          1          2             0             3     1
Residue 13t at the beginning of ./CG.ff/aminoacids.rtp
Sorting it all out...

Back Off! I just backed up topol.top to ./#topol.top.2#
Processing chain 1 'X' (3 atoms, 3 residues)
Identified residue MET1 as a starting terminus.
Identified residue VAL3 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Checking for duplicate atoms....
Now there are 3 residues with 3 atoms
Making bonds...
No bonds
Generating angles, dihedrals and pairs...
Making cmap torsions...There are    0 dihedrals,    0 impropers,    0 angles
             0 pairs,        0 bonds and     0 virtual sites
Total mass 319.420 a.m.u.
Total charge 1.000 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.2#

Writing coordinate file...

Back Off! I just backed up 60proc.pdb to ./#60proc.pdb.2#
                --------- PLEASE NOTE ------------
You have successfully generated a topology from:3Carbons.pdb.
The CG force field is used.
                --------- ETON ESAELP ------------

gcq#304: "Gabba Gabba Hey!" (The Ramones)

It stated that there are no angles.
However in my ffbonded.itp which i ncluded in my forcefield.itp

[ angletypes ]
; i  j  k funct th0  C0  C1  C2  C3  C4
CME    CSE    CVA    6    0    0.0680894    -0.0328291000    590330
-46.3    13

How Gromacs can read this angle?

In terms of bonds I want to use constraints, can I use in my ffbonded.itp [
costrainttypes] or add them automatically after?


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