[gmx-users] Virtual Sites + Capped Termini

[Joan Clark Nicolas]

Hi again!
I think I have solved the problem adding the following lines to the  [
constrainttypes ] section of ffbonded.itp:

; constraints for capped termini
  MCH3  C       2    0.166426
  MCH3  C       2    0.166426
  N     MCH3    2    0.166426
  N     MCH3    2    0.166426

where 0.166426 is the constraint parameter for rigid CH3 groups.

Then I change the names of my Virtual Sites in the capped termini from MCH1
and MCH2 to MCH3 and it runs fine, but I am not sure that I am choosing the
correct parameters, especially for the N-MCH3 bond.

What do you think?

Thanks!

*Joan Clark i Nicolas*

2015-10-22 17:41 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 10/22/15 9:05 AM, Joan Clark Nicolas wrote:
>
>> Dear gmx users,
>>
>> I am trying to simulate a protein-ligand system in gromacs 5.1 with capped
>> termini and using Virtual Sites.
>> When I try to generate the tpr file with grompp, it seems that it is
>> missing some constraint parameters for the bonds of C from ACE and N from
>> NME with their respective virtual sites. The error I am receiving is the
>> one that follows:
>>
>>
>> *ERROR 1 [file topol.top, line 8967]:*
>> *  No default Constr. No Conn. types*
>>
>>
>> *ERROR 2 [file topol.top, line 8968]:*
>> *  No default Constr. No Conn. types*
>>
>>
>> *ERROR 3 [file topol.top, line 9505]:*
>> *  No default Constr. No Conn. types*
>>
>>
>> *ERROR 4 [file topol.top, line 9506]:*
>> *  No default Constr. No Conn. types*
>>
>> where errors 1 and 2 correspond to ACE C-VS bonds and errors 3 and 4
>> correspond to NME N-VS bonds. Can you tell me what am I doing wrong?
>>
>>
> Probably nothing, but not all constraint types are necessarily defined,
> especially for capped termini.  You will have to calculate appropriate
> [constrainttypes] for ffbonded.itp and add them.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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