Re: [AMBER] urea force field

From: Carlos Romero <>
Date: Fri, 20 Nov 2015 15:23:12 -0600

Hi dear Jason. Thanks a lot again

I have tried what you recommend me. I follow the next procedure

loadamberparams frcmod.urea
savepdb UREABOX ureabox8M.pdb

Then I opened ureabox8M.pdb and selected only one residue and copy as a
New file, called ureabox8M.pdb.

I opened again xleap and type the follow
loadamberparams frcmod.urea
Ure = loadpdb ureabox8M.pdb.
Saveamberparm Ure urea.prmtop urea.inpcrd
But appears the next message

FATAL: ÁTOM .R <URE 1>.A <C 1> does not have a type
FATAL: ÁTOM .R <URE 1>.A <N1 2> does not have a type
FATAL: ÁTOM .R <URE 1>.A <N2 3> does not have a type
FATAL: ÁTOM .R <URE 1>.A <O 4> does not have a type
FATAL: ÁTOM .R <URE 1>.A <H1 5> does not have a type
FATAL: ÁTOM .R <URE 1>.A <H2 6> does not have a type
FATAL: ÁTOM .R <URE 1>.A <H3 7> does not have a type
Failed to generate parameters
Parameter file was not saved

Also, I tried loading file You sent me and I got the same

Moreover , a colleague did me the favor of getting to RED - TOOLS the mol2
file for urea. I did frcmod file with parmchk And when I load mol2 and
frcmod it works, I can save prmtop and inpcrd files. But when I save pdb
file and tried to load the same pdb file, happens the same error, I
can't save prmtop and inpcrd files.

I appreciate a lot your help.

El nov. 19, 2015 9:29 AM, "Jason Swails" <> escribió:

> On Thu, Nov 19, 2015 at 9:47 AM, Carlos Romero <>
> 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
> > 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 ( 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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Received on Fri Nov 20 2015 - 13:30:03 PST
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