[gmx-users] Angles not read
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
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
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
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
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
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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