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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>>
>>
>>
>> --
>> 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 Fri Apr 03 2015 - 05:30:03 PDT
