Dear all
I have used hemeall files from
http://www.pharmacy.manchester.ac.uk/bryce/amber
these are i steps adopted. i am having difficulty in saving input copdinate
and topology file.
[root.localhost hemeall]# tleap -f leaprc.ff99SB
-I: Adding /opt/amber10/dat/leap/prep to search path.
-I: Adding /opt/amber10/dat/leap/lib to search path.
-I: Adding /opt/amber10/dat/leap/parm to search path.
-I: Adding /opt/amber10/dat/leap/cmd to search path.
-f: Source leaprc.ff99SB.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: /opt/amber10/dat/leap/cmd/leaprc.ff99SB
Log file: ./leap.log
Loading parameters: /opt/amber10/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters: /opt/amber10/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /opt/amber10/dat/leap/lib/all_nucleic94.lib
Loading library: /opt/amber10/dat/leap/lib/all_amino94.lib
Loading library: /opt/amber10/dat/leap/lib/all_aminoct94.lib
Loading library: /opt/amber10/dat/leap/lib/all_aminont94.lib
Loading library: /opt/amber10/dat/leap/lib/ions94.lib
Loading library: /opt/amber10/dat/leap/lib/solvents.lib
> source leaprc.gaff
----- Source: /opt/amber10/dat/leap/cmd/leaprc.gaff
----- Source of /opt/amber10/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /opt/amber10/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June,
2003)
> loadamberparams frcmod.hemall
Loading parameters: ./frcmod.hemall
Reading force field modification type file (frcmod)
Reading title:
Force field modifcations for all-atom heme
> loadamberprep heme_all.prepin
Loading Prep file: ./heme_all.prepin
(no charges read on atoms lines in Heme residue ALL ATOM, Yves names,
Bayly)modified
> loadamberparams BHF.frcmod
Loading parameters: ./BHF.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> loadamberprep BHF.prepin
Loading Prep file: ./BHF.prepin
> nitu= loadpdb cyp1a1.pdb
Loading PDB file: ./cyp1a1.pdb
total atoms in file: 4173
Leap added 4140 missing atoms according to residue templates:
4140 H / lone pairs
> saveamberparm nitu cyp.prmtop cyp.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: 2.000000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
For atom: .R<HEM 513>.A<NA 2> Could not find type: NP
For atom: .R<HEM 513>.A<NB 23> Could not find type: NO
For atom: .R<HEM 513>.A<CBB 32> Could not find type: CX
For atom: .R<HEM 513>.A<NC 39> Could not find type: NP
For atom: .R<HEM 513>.A<CBC 48> Could not find type: CX
For atom: .R<HEM 513>.A<ND 55> Could not find type: NO
Parameter file was not saved.
>
please suggest me.
i am very thankful for the previous responses.
On Thu, Oct 14, 2010 at 5:07 PM, case <case.biomaps.rutgers.edu> wrote:
> On Thu, Oct 14, 2010, Nitu Bansal wrote:
> > Reading force field modification type file (frcmod)
> > Reading title:
> > Force field modifcations for united atom heme, plus flexible water
> > WARNING: expected Improper Torsion PK>0 (0.000000)
> > Here is the Improper Torsion line in question:
> > X CC CC X 0 0.000 180.000 2.000
> > WARNING: expected Improper Torsion PK>0 (0.000000)
> > Here is the Improper Torsion line in question:
> > X CB NO X 0 0.000 180.000 2.000
> > WARNING: expected Improper Torsion PK>0 (0.000000)
> > Here is the Improper Torsion line in question:
> > X CB NP X 0 0.000 180.000 2.000
> > WARNING: expected Improper Torsion PK>0 (0.000000)
> > Here is the Improper Torsion line in question:
> > X CB CC X 0 0.000 180.000 2.000
>
> These are just informational messages...leap is asking if you really want
> an
> improper torsion with zero force constant. In this case, you do.
>
> ...dac
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Nitu Bansal
M.S Pharm III Sem
Research Scholar
Center for Pharmacoinformatics
S.A.S Nagar NIPER Mohali (Chandigarh)
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Received on Thu Oct 14 2010 - 11:30:04 PDT
