[gmx-users] Angles not read

Steven Neumann s.neumann08 at gmail.com
Mon Jun 10 15:22:46 CEST 2013 

On Mon, Jun 10, 2013 at 2:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/10/13 9:11 AM, Steven Neumann wrote:
>
>> Thank you Justing. Last question - each of my amino acid is one bead. How
>> can I specify [angles ] between atoms corresponding to different residues?
>> Shall I add it at the end of my rtp entry with all amino acids?
>>
>>
> Each .rtp entry should only contain one bead, right?  The only way to
> define angles for such a system is to use +/- prefixes for succeeding and
> preceding residues (beads).
>
> -Justin
>

Yes, indeed. Can you provide me the example of such +/-?


>
>
>> On Mon, Jun 10, 2013 at 2:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> 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
>>>
>>> --
>>> ==============================****==========
>>>
>>>
>>> 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://vt.edu/Pages/Personal/justin>
>>> <h**ttp://www.bevanlab.biochem.vt.**edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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