[gmx-users] Angles not read

[Steven Neumann]

On Mon, Jun 10, 2013 at 1:55 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/10/13 8:53 AM, Steven Neumann wrote:
>
>> On Mon, Jun 10, 2013 at 1:44 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 6/10/13 8:42 AM, Justin Lemkul wrote:
>>>
>>>
>>>>
>>>> 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.
>>>>
>>>>
>>>>  Thinking a bit more though, it's probably a lot easier to define bonds
>>> and
>>> let pdb2gmx do the work for you.  Using:
>>>
>>> constraints = all-bonds
>>> constraint-algorithm = shake
>>>
>>> will turn all bonds in the topology into constraints, which sounds like
>>> exactly what you want to do.
>>>
>>>
>>> -Justin
>>>
>>>
>> Thank you. But specifying [ bonds ] in my rtp file without force constant?
>>
>
> Entries need to be syntactically correct, but the force constant is
> completely irrelevant if you are constraining all bonds.
>
>
>  Shall i remove [ bonds ] from my top file then?
>>
>>
> What?  Without [bonds], you can't do what I'm suggesting.  If you don't
> have [bonds], you have to write [constraints] and [angles] (and any other
> bonded directories) manually.
>

I am saying about removing them from top after pdb2gmx just to bring [
angles ] to top - I do not want to have a harmonic or any potential for
bonds.


>
> -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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