[gmx-users] Angles not read

[Steven Neumann]

On Mon, Jun 10, 2013 at 1:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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]?


I want to use constraints with SHAKE as bonds...no harmonic bonds. In this
case pdb2gmx will never create angles? Shall I also manually add [ angles ]
to my top then?


>
>
>  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].
>

I can manually add [ constraints ] to my top after processing with pdb2gmx

>
> -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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