[gmx-users] Angles not read

Justin Lemkul jalemkul at vt.edu
Mon Jun 10 15:24:29 CEST 2013 


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

>
>>
>>
>>> 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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-- 
========================================

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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