On Thu, Nov 19, 2015 at 9:47 AM, Carlos Romero <carlos.rom.74he.gmail.com>
wrote:
> Hi dear Karl. Thanks a lot for your answer.
>
> The problem is when I try to save prmtop and inpcrd files, appears the
> next message:
>
> Couldn't find angle and dihedrals params.
> The file was not saved.
> I knew There was a red - data base in http://q4md-forcefieldtools.org
> which contained parameters for urea, but it don't exist anymore.
> But I am going to Check the paper you recomend me.
>
> Thanks a lot again.
>
I tried the urea parameters from frcmod.urea and the residue template
inside UREABOX (8Mureabox.off) and the prmtop file saved just fine. So as
long as you use the same atom typing for the urea atoms as is used in
UREABOX, then loading frcmod.urea should be all that's needed to generate a
working topology file. This file, from what I could tell, was prepared in
2002, and you may need to check the resulting parameters to make sure that
the urea molecule behaves sensibly (but that is true regardless of where
you get your parameters from).
The only trick to using a single urea molecule (instead of a 8 M solution)
is to extract a library file (either mol2 file or OFF) that contains
an isolated URE residue. I have attached an OFF file that contains this
residue (which I generated from ParmEd by extracting one of the URE
residues from the UREABOX unit).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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- application/octet-stream attachment: urea.off
Received on Thu Nov 19 2015 - 07:30:02 PST
