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>:
>>
>> 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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>> >>> >> 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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>> >>>
>> >>
>> >>
>> >>
>> >> --
>> >> 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 - 06:30:02 PDT
