On Wed, May 18, 2011 at 10:38 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Thank you Jason,
>
> But let me see if I understood well.
>
> I moved the library and forcefield files generated for the original
> ligand.prmtop to a new directory. These files are:
> ligand.frcmod
> ligand.lib
> sqm.in
> sqm.out
>
You only need ligand.frcmod and ligand.lib
>
> I also moved in the same directory the ANTECHAMBER* files as well as the
> ligand.mol2 file generated by ANTECHAMBER originally.
>
You don't need any of these files if you generated a .lib file using
"saveoff" in leap.
>
> I started tleap:
>
>
> tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
>
> source leaprc.gaff
>
Did you load the ligand.lib and ligand.frcmod files here? If not, you'll
probably be in trouble...
>
>
> set default PBradii mbondi2
>
> Loaded the NEW protein pdb (protein+WAT) and saved the parameter files
>
> Did the same for the complex (protein+WAT+Ligand).
>
> I then tried to visualise
>
With xleap? Via "edit"?
>
> LIGAND=loadmol2 ligand.mol2
>
> In both cases I got some 430 warnings of the type:
>
> WARNING: There is a bond of 0.371657 angstroms between:
> ------- .R<LYS 124>.A<CD 11> and .R<LYS 124>.A<HD2 12>
> WARNING: There is a bond of 0.359783 angstroms between:
> ------- .R<LYS 124>.A<CD 11> and .R<LYS 124>.A<HD3 13>
>
These are expected based on the reasoning I gave at first. Therefore,
they're safe to ignore, since you know where they're coming from. Like I
said, the starting structure will be crap, and you won't want to use the
resulting inpcrd file for anything, but since the topology file is all
you're interested in, you're fine.
>
> -- ignoring the warnings.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> Building improper torsion parameters.
> total 437 improper torsions applied
> Building H-Bond parameters.
> Not Marking per-residue atom chain types.
>
> ====================================
>
> Needless to say that when I used the generated complex.prmtop file to
> visualise the PROCESSED trajectory, the result was ..... shall we say
> disappointing.
>
Then the number of atoms must be incompatible. If you aren't already using
NetCDF trajectories, I encourage you to do so, as it catches
incompatibilities that ASCII files won't catch (like, for instance, if you
have BOX coordinates and choose the wrong type of trajectory, or the number
of atoms/waters don't match).
Ultimately, there are a *lot* of things that can cause this effect, and I
can't tell from the given information what's causing it.
All the best,
Jason
> Sorry to bother you with this but I'm rather stuck.
>
> Have a good evening
>
> George
>
> On May 18, 2011, at 9:49 PM, Jason Swails wrote:
>
> > 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>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 18 2011 - 16:30:02 PDT
