On 6/10/13 8:23 AM, Steven Neumann wrote:
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
remove_dih
1 1 1 2 0 3 1
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?
[angletypes] simply define possible interactions, but are not used unless there
are [angles] in the .rtp that use them. pdb2gmx writes angles based on bonds,
but if you note above, there are zero bonds, so pdb2gmx cannot write any angles.
Does your .rtp entry specify [angles] but no [bonds]?
In terms of bonds I want to use constraints, can I use in my ffbonded.itp [
costrainttypes] or add them automatically after?
You would need [constraints] in your .top file, not [constrainttypes] (same
hierarchy as described above with angles). Usually .mdp keywords serve better
than topology modifications in the case of constraints, unless you're only
constraining a subset of atoms within a single [moleculetype].
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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