[gmx-users] Virtual sites error

[Timofey Tyugashev]

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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