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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>> >
>> >
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>
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Received on Fri Apr 03 2015 - 05:00:02 PDT
