You can use the average PDB, just make sure you use the same library files
and force field files for the new leap script as you did for the original
one when you built the system in the first place.
That is, there is *no* need to re-run antechamber (just use the results from
the first time you ran it).
HTH,
Jason
On Wed, May 18, 2011 at 9:27 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Many thanks Jason.
>
> Below is the script I used to process the original trajectory files.
>
> closest.in
>
> trajin prod_2ns.mdcrd
> trajin prod_4ns.mdcrd
> trajout prod_closest_WAT.mdcrd
> center :1-142
> image familiar
> solvent byres :WAT
> closest 1 :142
> strip :Na+
> average aver.pdb pdb
>
> Is there better way of generating a prmtop files for <closest_WAT.mdcrd> ?
>
> I understand that I should use these new files (ligand.prmtop;
> protein/WAT.prmtop; protein/WAT/ligand.prmtop) with MMPBSA.py
>
> Many thanks for your advice
>
> George
>
>
> On May 18, 2011, at 9:18 PM, Jason Swails wrote:
>
> > Average PDBs are very often horrible starting structures for antechamber,
> since rotationally degenerate atoms are superimposed, and an average tends
> to be distorted for a QM starting structure.
> >
> > Moreover, can't you reuse the prep or off files created for the original
> prmtop? If you don't, you won't get compatible charges for the original
> system.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> >
> > On May 18, 2011, at 2:24 PM, George Tzotzos <gtzotzos.me.com> wrote:
> >
> >> Hi everybody,
> >>
> >> I've generated an average pdb structure from a processed mdcrd file. I
> intend to use this average structure to generate topology files to visualise
> the processed trajectory.
> >>
> >> The average structure is attached. It consists of a receptor, ligand and
> one water molecule (closest to the ligand).
> >>
> >> I extracted from this average structure the ligand and save it as ligand
> pdb.
> >>
> >> I then tried to generate a mol2 file by using the following command:
> >>
> >> antechamber -i ligand.pdb -fi pdb -o bal.mol2 -fo mol2 -c bcc -s 2
> >>
> >> I got the following error message
> >>
> >> Warning: the assigned bond types may be wrong, please :
> >> (1) double check the structure (the connectivity) and/or
> >> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> >> (3) increase PSCUTOFF in define.h and recompile bondtype.c
> >> Be cautious, use a large value of PSCUTOFF (>100) will significantly
> increase the computation time
> >>
> >> Error: cannot run "/Users/gt/Programs/amber11/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> judgebondtype() of antechamber.c properly, exit
> >>
> >> I also tried the following.
> >>
> >> Opened ligand.pdb in Chimera and save it as ligand2.pdb (This created
> new connectivities).
> >>
> >> I re-run antechamber and got:
> >>
> >> Running: /Users/tzotzos/Programs/amber11/bin/bondtype -j full -i
> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> >> Running: /Users/tzotzos/Programs/amber11/bin/atomtype -i
> ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> >>
> >> Total number of electrons: 132; net charge: 0
> >>
> >> Running: /Users/tzotzos/Programs/amber11/bin/sqm -O -i sqm.in -o
> sqm.out
> >> Error: cannot run "/Users/tzotzos/Programs/amber11/bin/sqm -O -i sqm.in-o sqm.out" of bcc() in charge.c properly, exit
> >>
> >> Your help in solving this problem will be greatly appreciated.
> >>
> >> Best regards
> >>
> >> George
> >>
> >> <ligand.pdb>
> >>
> >>
> >>
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed May 18 2011 - 13:00:02 PDT
