Re: [AMBER] create urea molecule.

From: FyD <>
Date: Sat, 12 Feb 2011 08:38:15 +0100

Dear subrata,

Urea is in R.E.DD.B.

regards, Francois

Result(s) for search by Molecule name urea
Project name Urea
Project code W-80
Summary of information Click Here
Files (related to the charge derivation procedure)
File name Molecule name Type of file Link
tripos1.mol2 Urea Tripos Download
mol1.pdb Urea PDB Download ----- RESP input Download ----- RESP input Download

Files the author wishes to provide
(not related to the charge derivation procedure)Script name Description Link
File 1 Convertion of Tripos mol2 file into AMBER OFF library Download
File 2 Convertion of Tripos mol2 file into CHARMM RTF or PSF library Download
File 3 Missing force field parameters Download
File 4 File to provide more information about the project Download
File 5 File to provide more information about the project Download

All files compressed in tar.bz2Project code Link
W-80 Download

Quoting subrata paul <>:

> Dear
> Amber User,
> I want create a urea molecule considering duffy paramerters.For that I
> created a lib and frcmod file .
> Then i save the top and crd file
> saveamberparm URE a1.prmtop a1.inpcrd
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 3 improper torsions applied
> Building H-Bond parameters.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
> res total affected
> URE 1
> )
> (no restraints)
> Residues lacking connect0/connect1 , why this is coming?
> without comcidering this massege , I tried to run a simpele minimization.
> $AMBERHOME/exe/sander -O -i min.n -o min.out -p ure.prmtop -c ure.inpcrd -r
> min.rst &
> but output file was not written Why??
> thanking you
> subrata

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Received on Sat Feb 12 2011 - 00:00:03 PST
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