[gmx-users] Virtual sites error

[Erik Marklund]

If memory serves me right, the atom type for the carbon in the thymine ring lacks default constraint lengths to the dummy masses. That combination of atom types are not used for aminoacids. You will need to calculate what constraint lengths yield the correct geometry for the CH3-group, which is quite doable. It is sometimes pointed out however, here and elsewhere, that no vsite parameters have been rigorously tested for nucleic acids, only for proteins (to my knowledge).

Kind regards,
Erik

> On 9 Oct 2015, at 11:55, Timofey Tyugashev <tyugashev at niboch.nsc.ru> wrote:
> 
> 
> This looks very strange that from the whole assortment of the molecules in the force field only a humble methyl group in thymine lacks proper definition causes such an error.
> Even nucleotides which I added myself to the force field files don't produce any errors
> Is there any way to remedy this without significant hassle? What things are exactly lacking?
>> ------------------------------
>> 
>> Message: 4
>> Date: Thu, 8 Oct 2015 11:15:17 +0000
>> From: Erik Marklund <erik.marklund at chem.ox.ac.uk>
>> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] Virtual sites error
>> Message-ID: <89AE0BEC-6D9F-49A0-83E2-5AD8D7734505 at chem.ox.ac.uk>
>> Content-Type: text/plain; charset="us-ascii"
>> 
>> Unfortunately, the parameters required for certain virtual sites in nucleic acids are not define in the force field files that are shipped with Gromacs.
>> 
>> Erik Marklund, PhD
>> Postdoctoral Research Fellow
>> Fulford JRF, Somerville College
>> 
>> Department of Chemistry
>> Physical & Theoretical Chemistry Laboratory
>> University of Oxford
>> South Parks Road
>> Oxford
>> OX1 3QZ
>> 
>>> On 7 Oct 2015, at 11:33, Timofey Tyugashev <tyugashev at niboch.nsc.ru> wrote:
>>> 
>>> Trying to add hydrogen virtual sites to the model (using -vsites h option in pdb2gmx) results in a salvo of error messages when running grommp to create .tpr file after the solvation:
>>> 
>>> ERROR 1 [file topol_DNA_chain_A2.itp, line 1033]:
>>>  No default Constr. No Conn. types
>>> 
>>> 
>>> ERROR 2 [file topol_DNA_chain_A2.itp, line 1034]:
>>>  No default Constr. No Conn. types
>>> 
>>> This lines in constraints section in the .itp file refer to pairs of two MCH3 and one MC atoms, which should serve (the way I understand the situation) as replacement methyl group in thymine. There are several more pairs of same errors corresponding to different thymine methyl groups in the DNA strands.
>>> 
>>> Here is the relevant sections of the itp file for the first two errors:
>>> 
>>> [ constraints ]
>>> ;  ai    aj funct            c0            c1
>>>    2     3     2
>>>  110   111     2
>>>  110   112     2
>>>  111   112     2
>>> 
>>> [ atoms ]
>>> 
>>>   110         CM    321     DT     C5    110     0.0025 12.01   ; qtot -2.867
>>>   111       MCH3    321     DT   MC71    111          0 7.517   ; qtot -2.867
>>>   112       MCH3    321     DT   MC72    111          0 7.517   ; qtot -2.867
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