Dear Subrata,
> I downloaded tripos1.mol2 file and convert in to amber off file.
You do not need to convert mol2 file into OFF (both formats have the
same role in your case); but you do need to add the FF atom types
corresponding to the FF of your choice.
See
http://q4md-forcefieldtools.org/REDDB/projects/W-80/script1.ff
(or use antechamber to add FF atom types)
> after that i converted into prmtop and inpcrd file and then minimize with
> sander command.
> still out put file is not written why?
This looks like a sander problem...
What is the error generated by sander?
Did you test sander after compilation?
If I run the "sander" command only I get:
[fyd.lynx ~]$ sander
Unit 5 Error on OPEN: mdin
> actually I want to construct rigid planer urea molecule.How?
I would read how the rigid TIP3P water model has been constructed first...
You could also read the article from Fox & Kollman J. Phys. Chem. B
1998, 102, 8070-8079. They worked on organic solvents as well....
regards, Francois
> 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 - 08:30:02 PST
