Dear sir
I downloaded tripos1.mol2 file and convert in to amber off file.
after that i converted into prmtop and inpcrd file and then minimize with
sander command.
still out put file is not written why?
actually I want to construct rigid planer urea molecule.How?
thanking you
subrata
On Sat, Feb 12, 2011 at 11:38 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear subrata,
>
> Urea is in R.E.DD.B.
> See http://q4md-forcefieldtools.org/REDDB/projects/W-80/
>
> 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
> input1.in ----- RESP input Download
> input2.in ----- 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 <paul.subrata34.gmail.com>:
>
> > 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 - 04:00:01 PST
