[gmx-users] Angles not read

[Justin Lemkul]

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

-- 
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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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