[gmx-users] special bond

[Justin Lemkul]

On 4/29/14, 12:01 PM, Nicola Staffolani wrote:
> OK, the use of the same name and type is a bit confusing, so it wasn't
> clear from the last post that this should work.
>
> ​I beg your pardon but I think I am doing confusing things because I am
> confused myself and that's why I am looking for help ;)​
>

Just making an observation that is actually very common - people often try to 
use names where they shouldn't.

>
> In this case, it should (though of course you will get fatal errors
> regarding missing angles unless you define suitable [angletypes], but
> that's a separate issue).
> ​
> Indeed I do get fatal errors regarding missing angles, but unfortunately
> the gb's corresponding to the special bonds the atoms are supposed to make
> are *not* there, this is the alarming point...
> ​

It would be helpful to see:

1. The actual error messages.
2. The lines of the topology to which they correspond.

The thing you should know is that the Gromos force fields work in a manner that 
is different from basically all the others in Gromacs.  The fact that "gb_99" 
doesn't show up in the .top file is actually not really a problem - the 
parameters will be looked up from [bondtypes].  The explicit use of gb_*, ga_*, 
etc. is merely a convenience.  One can always override whatever is listed in 
[bondtypes] by writing in their own parameters in the .top file.  Is grompp 
complaining about missing parameters (i.e. "no default bondtypes") for your 
special bond?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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