[gmx-users] Angles not read

[Steven Neumann]

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
>

I want my atoms to be constrained. I specified in my topology

[ constraints ]
1 2 0.4
2 3 0.4
etc.
 Shall use?

constraints = none
constraint-algorithm = shake

I do not have [ bonds ] in my topology


> --
> ==============================**==========
>
> 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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