Dear
Sir
I converted tripos1.mol2 file according to the the scrip11.ff of REDserver.
then ssaved the prmtop and inpcrd file. but still not output file was
written during minimization in sander.why?
thanking you
subrata
On Sat, Feb 12, 2011 at 8:28 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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 Tue Feb 15 2011 - 04:30:03 PST
