[gmx-users] Angles not read
Steven Neumann
s.neumann08 at gmail.com
Mon Jun 10 15:11:18 CEST 2013
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?
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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