[gmx-users] Re: prodrg on small molecule

[Dallas B. Warren]

> PRODRG Beta2 generated the results as following:
>  [ bonds ]
>  ;ai  aj  fu    c0          c1
>    1   2   1 0.153    334720.0 0.153    334720.0 ;   C18  C13
>    2   3   1 0.153    334720.0 0.153    334720.0 ;   C13  C12
> .............
> 
> 
> But in GROMOS96(43a1), should be like this:
> [ bonds ]
>  ;ai  aj  fu    c0          c1
>      1     2     2 gb_26
>      2     3     2 gb_26
> ............
> 
> So my question is should I change all the format as those in
> GROMOS96(43a1) style? If so, some of the bonds are not 
> defined in GROMOS96(43a1), so I should add these missing 
> bonds into it manually, right?

These are the same thing.  The gb_26 tells it to insert the bond details
into the topology, and those details look something like "0.153
334720.0 0.153    334720.0".  So whether they are all the same or not
doesn't matter.  Other than for consistency, reducing confusion etc.
And yes, you can add the missing bonds manually, just by defining
additional gb_# terms and others as required.

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9073
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.