[gmx-users] Angles not read
Justin Lemkul
jalemkul at vt.edu
Mon Jun 10 15:14:18 CEST 2013
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
>
> 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://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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