[AMBER] create urea molecule.

From: subrata paul <paul.subrata34.gmail.com>
Date: Sat, 12 Feb 2011 11:22:54 +0400

 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
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Received on Fri Feb 11 2011 - 23:30:02 PST
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