[gmx-users] Angles not read

Steven Neumann s.neumann08 at gmail.com
Mon Jun 10 15:27:34 CEST 2013


On Mon, Jun 10, 2013 at 2:24 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/10/13 9:22 AM, Steven Neumann wrote:
>
>> 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 +/-?
>>
>>
> Look in any .rtp file that comes with Gromacs.  In your case, it is even
> easier than an atomistic force field.
>
> -Justin
>

Obviously... sorry for this question.

Thank you.

Steven

>
>
>>
>>>
>>>  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<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<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://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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