>
> 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> 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>:
> > 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>:
> >> 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>
> >> 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
> >:
> >>> > 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:_e(%7B%7D,'cvml','jmsstarlight.gmail.com');>> 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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> >>> >> AMBER.ambermd.org
> >>> >> 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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> >>>
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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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> >> AMBER mailing list
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> >> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Apr 03 2015 - 08:30:04 PDT
