[gmx-users] Angles not read

[Justin Lemkul]

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

-- 
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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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