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>:
> 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
>>> >>> >>
>>> >>> >
>>> >>> >
>>> >>> > --
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>>> >>> imprisoned
>>> >>> > here could not dream of heaven?
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>>> >>
>>> >>
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>>> imprisoned
>>> >> here could not dream of heaven?
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Received on Mon Apr 06 2015 - 07:30:02 PDT
