[gmx-users] Virtual Sites + Capped Termini

[Justin Lemkul]

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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