[gmx-users] Angles not read

[Justin Lemkul]

On 6/11/13 5:59 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
>>
>
> I want my atoms to be constrained. I specified in my topology
>
> [ constraints ]
> 1 2 0.4
> 2 3 0.4
> etc.
>   Shall use?
>

You're missing a function type.

> constraints = none
> constraint-algorithm = shake
>
> I do not have [ bonds ] in my topology
>

Presumably it should work (pending the correction noted above).  Try it and see.

-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

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