Assuming that you've treated the trajectories all the same before or after
merging them, ie applying the same strip masks, etc, then there shouldn't
be a problem.
I don't think MMPBSA should care too much about where your coordinates are,
though it never hurts to autoimage and center your trajectory to a
reference. This seems more to be there's something present in the
trajectory or topology from the error message.
Best,
Kenneth
On Monday, April 6, 2015, James Starlight <jmsstarlight.gmail.com> wrote:
> one important suggestion regarding my issue:
>
> I've tried to make this type of mmgbsa for merged trajectory consisted
> of 3 trajectory (each of which has been calculated for same input
> prmtop file) using below script to cut it together:
>
> parm protein.parm7
> trajin md1.nc 100 last 1
> trajin md2.nc 100 last 1
> trajin md3.nc 100 last 1
> trajout merged_md1_2_3.nc netcdf
>
> should I provide here some reference also to superimpose all of those
> trajectories onto common reference? What also might be relevant?
>
> James
> ~
> ~
> ~
> ~
> ~
>
> 2015-04-06 15:12 GMT+02:00 James Starlight <jmsstarlight.gmail.com
> <javascript:;>>:
> > no no it was exactly paramtop of the whole system loaded with full
> > trajectory as you can found from
> >
> > 0: OR5P3_plus-carvone.parm7, 44513 atoms, 9262 res, box: Orthogonal,
> > 8970 mol, 8856 solvent, 5901 frames
> > just try to switch to the ambertools-14 and let you know about success
> >
> >
> >
> > James
> >
> > 2015-04-03 17:22 GMT+02:00 Kenneth Huang <kennethneltharion.gmail.com
> <javascript:;>>:
> >>>
> >>> how it would be possible to obtain some coordinates just from the
> >>> topology and trajectory using ambpdb? I'm working on cluster where
> >>> unfortunately there is no any visualization software.
> >>
> >>
> >> The general command for ambpdb is
> >>
> >> ambpdb -p topology.prmtop < restart.inpcrd > OutputName.pdb
> >>
> >> Usually I use it with the starting .inpcrd or .restrt files- I haven't
> >> tried it with a trajectory, but I assume that you can just save a single
> >> frame, and use that as your coordinate file for ambpdb. Alternatively,
> you
> >> can save a single frame and move it along with the topologies onto a
> local
> >> machine to try to visualize it there.
> >>
> >>
> >>> also I've load both prmtop and nc into the cpptraj and no mismatch has
> >>> been found
> >>
> >>
> >> I could be wrong, but it looks like you've selected the initial prmtop
> and
> >> your trajectory- try loading a stripped version of your trajectory
> (using
> >> the same masks that you chose in running ante-MMPBSA) and its
> corresponding
> >> complex prmtop. Since I assume you can load your initial
> prmtop/trajectory
> >> without issue, I'm thinking that the issue is somewhere in the
> >> complex.prmtop file.
> >>
> >> just noticed that on cluster I'm using amber-tools-13. Was some bug
> >>> within mmpbsa.py of amber-tools of this version?
> >>
> >>
> >> I'm not sure if AmberTools13 had any problems associated with this, so
> >> you'd have to wait for someone else to weigh in. That said, I'm usually
> in
> >> favor of using newer versions of AmberTools, ie AmberTools14, unless you
> >> have a specific reason not to.
> >>
> >> Best,
> >>
> >> Kenneth
> >>
> >> On Friday, April 3, 2015, James Starlight <jmsstarlight.gmail.com
> <javascript:;>> wrote:
> >>
> >>> also I've load both prmtop and nc into the cpptraj and no mismatch has
> >>> been found
> >>>
> >>> CPPTRAJ: Trajectory Analysis. V13.24
> >>> ___ ___ ___ ___
> >>> | \/ | \/ | \/ |
> >>> _|_/\_|_/\_|_/\_|_
> >>> INPUT: Reading Input from file xz.in
> >>> [parm OR5P3_plus-carvone.parm7]
> >>> AmberParm Title: [default_name]
> >>> Radius Set: modified Bondi radii (mbondi)
> >>> [trajin OR5P3_plus-carvone.nc netcdf 100 last 1]
> >>> [OR5P3_plus-carvone.nc] contains 6000 frames.
> >>> [trajout md_5p3_coumarin_md1_2.dcd dcd first]
> >>>
> >>> PARAMETER FILES:
> >>> 0: OR5P3_plus-carvone.parm7, 44513 atoms, 9262 res, box: Orthogonal,
> >>> 8970 mol, 8856 solvent, 5901 frames
> >>>
> >>> INPUT TRAJECTORIES:
> >>> 0: [OR5P3_plus-carvone.nc] is a NetCDF AMBER trajectory, Parm
> >>> OR5P3_plus-carvone.parm7 (Orthogonal box) (reading 5901 of 6000)
> >>> Coordinate processing will occur on 5901 frames.
> >>>
> >>>
> >>> just noticed that on cluster I'm using amber-tools-13. Was some bug
> >>> within mmpbsa.py of amber-tools of this version?
> >>>
> >>> J
> >>>
> >>> 2015-04-03 13:53 GMT+02:00 James Starlight <jmsstarlight.gmail.com
> <javascript:;>>:
> >>> > I've checked it- solvent has been stripped correctly! and yes I'm
> >>> > using the same prmtop which I've used as the input to produce
> >>> > trajectory
> >>> > residues from complex:
> >>> > %FORMAT(20a4)
> >>> > GLU ASP THR THR VAL CYS ALA ILE LEU PHE LEU VAL PHE LEU GLY ILE TYR
> VAL
> >>> VAL THR
> >>> > LEU MET GLY ASN ILE SER ILE ILE VAL LEU ILE ARG ARG SER HID HIP LEU
> HID
> >>> THR PRO
> >>> > MET TYR ILE PHE LEU CYS HID LEU ALA PHE VAL ASH ILE GLY TYR SER SER
> SER
> >>> VAL THR
> >>> > PRO VAL MET LEU MET SER PHE LEU ARG LYS GLH THR SER LEU PRO VAL ALA
> GLY
> >>> CYX VAL
> >>> > ALA GLN LEU CYS SER VAL VAL THR PHE GLY THR ALA GLH CYS PHE LEU LEU
> ALA
> >>> ALA MET
> >>> > ALA TYR ASP ARG TYR VAL ALA ILE CYS SER PRO LEU LEU TYR SER THR CYS
> MET
> >>> SER PRO
> >>> > GLY VAL CYS ILE ILE LEU VAL GLY MET SER TYR LEU GLY GLY CYS VAL ASN
> ALA
> >>> TRP THR
> >>> > PHE ILE GLY CYS LEU LEU ARG LEU SER PHE CYS GLY PRO ASN LYS VAL ASN
> HIP
> >>> PHE PHE
> >>> > CYX ASP TYR SER PRO LEU LEU LYS LEU ALA CYS SER HID ASP PHE THR PHE
> GLU
> >>> ILE ILE
> >>> > PRO ALA ILE SER SER GLY SER ILE ILE VAL ALA THR VAL CYS VAL ILE ALA
> ILE
> >>> SER TYR
> >>> > ILE TYR ILE LEU ILE THR ILE LEU LYS MET HID SER THR LYS GLY ARG HIE
> LYS
> >>> ALA PHE
> >>> > SER THR CYS THR SER HID LEU THR ALA VAL THR LEU PHE TYR GLY THR ILE
> THR
> >>> PHE ILE
> >>> > TYR VAL MET PRO LYS SER SER TYR SER THR ASP GLN ASN LYS VAL VAL SER
> VAL
> >>> PHE TYR
> >>> > THR VAL VAL ILE PRO MET LEU ASN PRO LEU ILE TYR SER LEU ARG ASN LYS
> GLU
> >>> ILE LYS
> >>> > GLY ALA LEU LYS ARG GLU LEU ARG ILE LYS ILE PHE SER MOL
> >>> >
> >>> > residues from receptor:
> >>> >
> >>> > %FORMAT(20a4)
> >>> > GLU ASP THR THR VAL CYS ALA ILE LEU PHE LEU VAL PHE LEU GLY ILE TYR
> VAL
> >>> VAL THR
> >>> > LEU MET GLY ASN ILE SER ILE ILE VAL LEU ILE ARG ARG SER HID HIP LEU
> HID
> >>> THR PRO
> >>> > MET TYR ILE PHE LEU CYS HID LEU ALA PHE VAL ASH ILE GLY TYR SER SER
> SER
> >>> VAL THR
> >>> > PRO VAL MET LEU MET SER PHE LEU ARG LYS GLH THR SER LEU PRO VAL ALA
> GLY
> >>> CYX VAL
> >>> > ALA GLN LEU CYS SER VAL VAL THR PHE GLY THR ALA GLH CYS PHE LEU LEU
> ALA
> >>> ALA MET
> >>> > ALA TYR ASP ARG TYR VAL ALA ILE CYS SER PRO LEU LEU TYR SER THR CYS
> MET
> >>> SER PRO
> >>> > GLY VAL CYS ILE ILE LEU VAL GLY MET SER TYR LEU GLY GLY CYS VAL ASN
> ALA
> >>> TRP THR
> >>> > PHE ILE GLY CYS LEU LEU ARG LEU SER PHE CYS GLY PRO ASN LYS VAL ASN
> HIP
> >>> PHE PHE
> >>> > CYX ASP TYR SER PRO LEU LEU LYS LEU ALA CYS SER HID ASP PHE THR PHE
> GLU
> >>> ILE ILE
> >>> > PRO ALA ILE SER SER GLY SER ILE ILE VAL ALA THR VAL CYS VAL ILE ALA
> ILE
> >>> SER TYR
> >>> > ILE TYR ILE LEU ILE THR ILE LEU LYS MET HID SER THR LYS GLY ARG HIE
> LYS
> >>> ALA PHE
> >>> > SER THR CYS THR SER HID LEU THR ALA VAL THR LEU PHE TYR GLY THR ILE
> THR
> >>> PHE ILE
> >>> > TYR VAL MET PRO LYS SER SER TYR SER THR ASP GLN ASN LYS VAL VAL SER
> VAL
> >>> PHE TYR
> >>> > THR VAL VAL ILE PRO MET LEU ASN PRO LEU ILE TYR SER LEU ARG ASN LYS
> GLU
> >>> ILE LYS
> >>> > GLY ALA LEU LYS ARG GLU LEU ARG ILE LYS ILE PHE SER
> >>> >
> >>> > how it would be possible to obtain some coordinates just from the
> >>> > topology and trajectory using ambpdb? I'm working on cluster where
> >>> > unfortunately there is no any visualization software.
> >>> >
> >>> > J.
> >>> >
> >>> > 2015-04-02 17:38 GMT+02:00 Kenneth Huang <
> kennethneltharion.gmail.com <javascript:;>>:
> >>> >> Okay, so the error here isn't with your topologies- those are fine.
> It's
> >>> >> that your topologies and coordinate files aren't matching up for
> some
> >>> >> reason. Assuming that they're the ones that you ran MD with, my best
> >>> guess
> >>> >> is that there's something leftover that you forgot to strip out
> when you
> >>> >> ran ante-MMPBSA?
> >>> >>
> >>> >> You can also try making a pdb file with ambpdb using the same
> inputs, or
> >>> >> loading your trajectory with the relative topology into VMD to see
> if it
> >>> >> works. If both of them fail, then something is missing from your
> >>> topologies
> >>> >> that's still in your trajectory.
> >>> >>
> >>> >> Best,
> >>> >>
> >>> >> Kenneth
> >>> >>
> >>> >> On Thu, Apr 2, 2015 at 11:08 AM, James Starlight <
> >>> jmsstarlight.gmail.com <javascript:;>>
> >>> >> wrote:
> >>> >>
> >>> >>> what I found on the bottom
> >>> >>>
> >>> >>>
> >>> >>> FATAL: NATOM mismatch in coord and topology files
> >>> >>>
> >>> >>>
> >>> >>> I've checked all topologies and it seems ok for me
> >>> >>>
> >>> >>> n atoms of complex.prmtop = n atoms of receptor.prmtop + n atoms of
> >>> >>> ligand.prmtop
> >>> >>>
> >>> >>> it;s strange because I don't see here where the coordinate file
> (smth
> >>> >>> like protein.inpcrd) are provided in the below mmgbsa input
> >>> >>>
> >>> >>> mpirun -np 16 MMPBSA.py.MPI -O -i mmgbsa.in -o
> >>> >>> mmgbsa_nm_OR5P3_quinoline.dat -sp
> >>> >>> /home/cmoon/argh/OR5P3_quinoline/protein.parm7 -cp
> >>> >>>
> >>> >>>
> >>>
> /home/cmoon/argh/OR5P3_quinoline/decomposition_OR5P3_quinoline/complex.prmtop
> >>> >>> -rp
> >>> >>>
> >>>
> /home/cmoon/argh/OR5P3_quinoline/decomposition_OR5P3_quinoline/receptor.prmtop
> >>> >>> -y /home/cmoon/argh/OR5P3_quinoline/md3.nc -lp
> >>> >>>
> >>> >>>
> >>>
> /home/cmoon/argh/OR5P3_quinoline/decomposition_OR5P3_quinoline/ligand.prmtop
> >>> >>> > progress.log 2>&1
> >>> >>>
> >>> >>>
> >>> >>>
> >>> >>> 2015-04-02 16:50 GMT+02:00 Kenneth Huang <
> kennethneltharion.gmail.com <javascript:;>
> >>> >:
> >>> >>> > James,
> >>> >>> >
> >>> >>> > Generally speaking, you can always make the stripped topologies
> you
> >>> need
> >>> >>> in
> >>> >>> > tleap, usually before you add ions and solvent, or you could just
> >>> reload
> >>> >>> > your starting structure into tleap and save it without
> solvent/ions.
> >>> That
> >>> >>> > said, ante-MMPBSA is good for when you don't have your starting
> >>> structure
> >>> >>> > anymore, or don't want to backtrack, or don't know what masks you
> >>> want to
> >>> >>> > use.
> >>> >>> >
> >>> >>> > As for your error, try checking the MMPBSA gb mdout file- it
> should
> >>> give
> >>> >>> > you a more descriptive error message.
> >>> >>> >
> >>> >>> > Best,
> >>> >>> >
> >>> >>> > Kenneth
> >>> >>> >
> >>> >>> > On Thursday, April 2, 2015, James Starlight <
> jmsstarlight.gmail.com <javascript:;>
> >>> >>> > <javascript:_e(%7B%7D,'cvml','jmsstarlight.gmail.com
> <javascript:;>');>> wrote:
> >>> >>> >
> >>> >>> >> Dear Friends!
> >>> >>> >>
> >>> >>> >> I've faced with the problem during mmgbsa analysis of my system:
> >>> >>> >>
> >>> >>> >>
> >>> >>> >>
> >>> >>> >> Firstly I have no problems with processing of initial
> protein.parm7
> >>> >>> >> obtained using
> >>> >>> >>
> >>> >>> >> ante-MMPBSA.py -p ${sim}/protein.parm7 -c
> >>> >>> >> ${sim}/decomposition_${simulation}/complex.prmtop -r
> >>> >>> >> ${sim}/decomposition_${simulation}/receptor.prmtop -l
> >>> >>> >> ${sim}/decomposition_${simulation}/ligand.prmtop -s
> >>> >>> >> :WAT:Cl-:NA+:K+:PPC -n :MOL
> >>> >>> >>
> >>> >>> >> Stripping :WAT:Cl-:NA+:K+:PPC (solvent) from original topology,
> >>> output
> >>> >>> >> is
> >>> >>> >>
> >>> >>>
> >>>
> /home/cmoon/total_decomp/OR5P3_androstenone/decomposition_OR5P3_androstenone/complex.prmtop
> >>> >>> >> Done stripping solvent!
> >>> >>> >>
> >>> >>> >> Creating receptor topology file by stripping :MOL from
> >>> >>> >>
> >>> >>> >>
> >>> >>>
> >>>
> /home/cmoon/total_decomp/OR5P3_androstenone/decomposition_OR5P3_androstenone/complex.prmtop
> >>> >>> >> Done creating receptor topology file!
> >>> >>> >>
> >>> >>> >> Creating ligand topology file by stripping !(:MOL) from
> >>> >>> >>
> >>> >>> >>
> >>> >>>
> >>>
> /home/cmoon/total_decomp/OR5P3_androstenone/decomposition_OR5P3_androstenone/complex.prmtop
> >>> >>> >> Done creating ligand topology file!
> >>> >>> >>
> >>> >>> >>
> >>> >>> >>
> >>> >>> >> but then during decomposition using mmgbsa.py I've obtained
> error at
> >>> >>> >> the begining of calculations:
> >>> >>> >> (here the input file consisted of paths because it was produced
> by
> >>> my
> >>> >>> >> bash script)
> >>> >>> >> mpirun -np 16 MMPBSA.py.MPI -O -i mmgbsa.in -o
> >>> >>> >> mmgbsa_nm_OR5P3_androstenone.dat -sp
> >>> >>> >> /home/cmoon/total_decomp/OR5P3_androstenone/protein.parm7 -cp
> >>> >>> >> complex.prmtop -rp receptor.prmtop -y
> >>> >>> >> /home/cmoon/total_decomp/OR5P3_androstenone/md1.nc
> >>> >>> >> /home/cmoon/total_decomp/OR5P3_androstenone/md2.nc
> >>> >>> >> /home/cmoon/total_decomp/OR5P3_androstenone/md3.nc -lp
> >>> ligand.prmtop >
> >>> >>> >> progress.log 2>&1
> >>> >>> >>
> >>> >>> >> ::
> >>> >>> >> Running calculations on normal system...
> >>> >>> >>
> >>> >>> >> Beginning GB calculations with
> /home/cmoon/Prog/amber12/bin/sander
> >>> >>> >> calculating complex contribution...
> >>> >>> >> CalcError: /home/cmoon/Prog/amber12/bin/sander failed with
> prmtop
> >>> >>> >> complex.prmtop!
> >>> >>> >> Error occured on rank 3.
> >>> >>> >> Exiting. All files have been retained.
> >>> >>> >> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
> >>> >>> >> APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
> >>> >>> >>
> >>> >>> >> I've checked all prmtop files used here but have not found any
> >>> errors
> >>> >>> >> here (the atom numbers and its composition is correct in all 3
> >>> >>> >> topologies made by ante-mmbsa). Could someone suggest me some
> >>> >>> >> resolution if the issue and alternative method to made stripped
> >>> >>> >> topologies avoiding ante-mmbsa?
> >>> >>> >>
> >>> >>> >> Thanks!!
> >>> >>> >>
> >>> >>> >> James
> >>> >>> >>
> >>> >>> >> _______________________________________________
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> >>> >>> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>> >>> >>
> >>> >>> >
> >>> >>> >
> >>> >>> > --
> >>> >>> > Ask yourselves, all of you, what power would hell have if those
> >>> >>> imprisoned
> >>> >>> > here could not dream of heaven?
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> >>> >>>
> >>> >>
> >>> >>
> >>> >>
> >>> >> --
> >>> >> Ask yourselves, all of you, what power would hell have if those
> >>> imprisoned
> >>> >> here could not dream of heaven?
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Received on Mon Apr 06 2015 - 07:30:03 PDT
