[gmx-users] Angles not read

[Justin Lemkul]

On 6/10/13 8:40 AM, Steven Neumann wrote:
> 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?
>

Yes, because in the absence of bonds, even [angles] in .rtp entries are ignored.

>
>>
>>
>>   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
>

Yes.

-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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