[gmx-users] Angles not read

[Justin Lemkul]

On 6/10/13 9:04 AM, Steven Neumann wrote:
> 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.
>

I suppose you can do that, but why bother?  If you want to constrain all bonds 
with SHAKE, see above.  There will be no harmonic potential anywhere if all 
bonds are constrained.

-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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