Hello Fellow amber users
I am an undergraduate researcher so forgive my lack of knowledge in this
area but I was wondering if you can help me out.
I am running into a problem running MMPB/GBSA calculations and I was
wondering if anyone can give me some tips.
To start off: I built a membrane around a GPCR with a ligand already placed
in it using CHARMMGUI and there force fields. I then took there outputs, in
the amber format, and ran MD. Using the output pdb from what CHARMGUI gave
me I then used an ante-mmpbsa.py script as follows:
ante-MMPBSA.py -p step5_charmm2amber.parm7 -c complex.prmtop -r
receptor.prmtop -l ligand.prmtop -n":279" -s":TIP3:MEMB:CLA:WAT:POPC"
But it turns out that PDB is incorrect and it is actually 277 that is the
ligand. So there may be something fishy here I am just not sure.
As you can tell I am not to sure about the -s command so I covered all my
bases.(IF you can help me out here that would be helpful, I think I only
need the residue names but I am not sure.) I then took the given prmtop
files which I opened and compared atom counts to the pdb file and they
check out. I also compared to my best extent the rest of the file to see if
there was anything amiss and to me it checks out. I then ran MMPBSA using
this script:
mpirun -np 20 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o test.dat -sp
step5_charmm2amber.parm7 -cp complex.prmtop -rp receptor.prmtop -lp
ligand.prmtop -y prod.nc -eo excel_out.csv
I receive an error saying there is something wrong with my complex.prmtop
and the calculation failed.
Here is the error :
Running calculations on normal system...
Beginning GB calculations with /usr/local/amber16/bin/sander
calculating complex contribution...
File "/usr/local/amber16/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /usr/local/amber16/bin/sander failed with prmtop complex.prmtop!
Error occured on rank 5.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 5
File "/usr/local/amber16/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /usr/local/amber16/bin/sander failed with prmtop complex.prmtop!
Error occured on rank 6.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 25614 RUNNING AT localhost.localdomain
= EXIT CODE: 1
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
=================================================================================
Before I submit my PB I always check GB so that is why you only see the GB
part. When I check the _MMPBSA_ files I read this error FATAL: NATOM
mismatch in coord and topology files.
I tried this many different ways and got a couple of people to retry it for
me to see if I did something wrong, and we keep getting this error.
So I tried another approach.
I decided to create .parm7 files using cpptraj tool. With scripts that look
like this:
trajin prod.nc 1 1 1
strip :TIP3 outprefix strip
strip :CLA outprefix strip
strip :POPC outprefix strip
strip :MEMB outprefix strip
strip :WAT outprefix strip
strip :ALA outprefix strip
strip :GLY outprefix strip
strip :ILE outprefix strip
strip :LEU outprefix strip
strip :PRO outprefix strip
strip :VAL outprefix strip
strip :PHE outprefix strip
strip :TRP outprefix strip
strip :TYR outprefix strip
strip :ASP outprefix strip
strip :GLU outprefix strip
strip :ARG outprefix strip
strip :HIS outprefix strip
strip :LYS outprefix strip
strip :SER outprefix strip
strip :THR outprefix strip
strip :CYS outprefix strip
strip :MET outprefix strip
strip :ASN outprefix strip
strip :GLN outprefix strip
strip :HSD outprefix strip
autoimage
rms first :1-277.CA,C,N
trajout ligand.pdb pdb nobox
The scripts vary from what I want to make so the example above is the pure
ligand. I also made sure under:
%FLAG FORCE_FIELD_TYPE
%FORMAT(i2,a78)
It had this:
2 >>>> CHARMM36 All-Hydrogen Parameter File for Proteins
<<<<<<<<<<
2 CHARMM: >>>>>>>>>>>> All-hydrogen parameters used in the
<<<<<<<<<<<<<<<<
Then using this script:
mpirun -np 8 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o test.dat -sp
step5_charmm2amber.parm7 -cp complex.parm7 -rp receptor.parm7 -lp
ligand.parm7 -y prod.nc -eo excel_out.csv
I received this error:
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
Loading and checking parameter files for compatibility...
File "/usr/local/amber16/bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
572, in loadcheck_prmtops
File "/usr/local/amber16/bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
572, in loadcheck_prmtops
FILES.receptor_prmtop, FILES.ligand_prmtop)
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 98, in __init__
FILES.receptor_prmtop, FILES.ligand_prmtop)
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 98, in __init__
self.complex_prmtop = LoadParm(complex_prmtop)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/readparm.py",
line 66, in LoadParm
parm = parm.view_as(ChamberParm)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/amberformat.py",
line 420, in view_as
self.complex_prmtop = LoadParm(complex_prmtop)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/readparm.py",
line 66, in LoadParm
parm = parm.view_as(ChamberParm)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/amberformat.py",
line 420, in view_as
return cls.from_rawdata(self)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 259, in from_rawdata
return cls.from_rawdata(self)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 259, in from_rawdata
inst.initialize_topology()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 103, in initialize_topology
inst.initialize_topology()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 103, in initialize_topology
AmberParm.initialize_topology(self, xyz, box)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 213, in initialize_topology
self.load_structure()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 143, in load_structure
super(ChamberParm, self).load_structure()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 498, in load_structure
self._check_section_lengths()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 423, in _check_section_lengths
check_length('LENNARD_JONES_14_ACOEF', ntypes*(ntypes+1)//2)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 407, in check_length
(key, len(self.parm_data[key]), length))
AmberError: FLAG LENNARD_JONES_14_ACOEF has 3160 elements; expected 1770
Exiting. All files have been retained.
AmberParm.initialize_topology(self, xyz, box)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 213, in initialize_topology
self.load_structure()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 143, in load_structure
super(ChamberParm, self).load_structure()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 498, in load_structure
self._check_section_lengths()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 423, in _check_section_lengths
check_length('LENNARD_JONES_14_ACOEF', ntypes*(ntypes+1)//2)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 407, in check_length
(key, len(self.parm_data[key]), length))
AmberError: FLAG LENNARD_JONES_14_ACOEF has 3160 elements; expected 1770
Exiting. All files have been retained.
File "/usr/local/amber16/bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
572, in loadcheck_prmtops
FILES.receptor_prmtop, FILES.ligand_prmtop)
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 98, in __init__
self.complex_prmtop = LoadParm(complex_prmtop)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/readparm.py",
line 66, in LoadParm
parm = parm.view_as(ChamberParm)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/amberformat.py",
line 420, in view_as
return cls.from_rawdata(self)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 259, in from_rawdata
inst.initialize_topology()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 103, in initialize_topology
AmberParm.initialize_topology(self, xyz, box)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 213, in initialize_topology
self.load_structure()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 143, in load_structure
super(ChamberParm, self).load_structure()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 498, in load_structure
self._check_section_lengths()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 423, in _check_section_lengths
check_length('LENNARD_JONES_14_ACOEF', ntypes*(ntypes+1)//2)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 407, in check_length
(key, len(self.parm_data[key]), length))
AmberError: FLAG LENNARD_JONES_14_ACOEF has 3160 elements; expected 1770
Exiting. All files have been retained.
File "/usr/local/amber16/bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
572, in loadcheck_prmtops
FILES.receptor_prmtop, FILES.ligand_prmtop)
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 98, in __init__
self.complex_prmtop = LoadParm(complex_prmtop)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/readparm.py",
line 66, in LoadParm
parm = parm.view_as(ChamberParm)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/amberformat.py",
line 420, in view_as
return cls.from_rawdata(self)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 259, in from_rawdata
inst.initialize_topology()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 103, in initialize_topology
AmberParm.initialize_topology(self, xyz, box)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 213, in initialize_topology
self.load_structure()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 143, in load_structure
super(ChamberParm, self).load_structure()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 498, in load_structure
self._check_section_lengths()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 423, in _check_section_lengths
check_length('LENNARD_JONES_14_ACOEF', ntypes*(ntypes+1)//2)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 407, in check_length
(key, len(self.parm_data[key]), length))
AmberError: FLAG LENNARD_JONES_14_ACOEF has 3160 elements; expected 1770
Exiting. All files have been retained.
File "/usr/local/amber16/bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
572, in loadcheck_prmtops
FILES.receptor_prmtop, FILES.ligand_prmtop)
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 98, in __init__
self.complex_prmtop = LoadParm(complex_prmtop)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/readparm.py",
line 66, in LoadParm
parm = parm.view_as(ChamberParm)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/amberformat.py",
line 420, in view_as
return cls.from_rawdata(self)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 259, in from_rawdata
inst.initialize_topology()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 103, in initialize_topology
AmberParm.initialize_topology(self, xyz, box)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 213, in initialize_topology
self.load_structure()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 143, in load_structure
super(ChamberParm, self).load_structure()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 498, in load_structure
self._check_section_lengths()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 423, in _check_section_lengths
check_length('LENNARD_JONES_14_ACOEF', ntypes*(ntypes+1)//2)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 407, in check_length
(key, len(self.parm_data[key]), length))
AmberError: FLAG LENNARD_JONES_14_ACOEF has 3160 elements; expected 1770
Exiting. All files have been retained.
File "/usr/local/amber16/bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
572, in loadcheck_prmtops
FILES.receptor_prmtop, FILES.ligand_prmtop)
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 98, in __init__
self.complex_prmtop = LoadParm(complex_prmtop)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/readparm.py",
line 66, in LoadParm
parm = parm.view_as(ChamberParm)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/amberformat.py",
line 420, in view_as
return cls.from_rawdata(self)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 259, in from_rawdata
inst.initialize_topology()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 103, in initialize_topology
AmberParm.initialize_topology(self, xyz, box)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 213, in initialize_topology
self.load_structure()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 143, in load_structure
super(ChamberParm, self).load_structure()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 498, in load_structure
self._check_section_lengths()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 423, in _check_section_lengths
check_length('LENNARD_JONES_14_ACOEF', ntypes*(ntypes+1)//2)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 407, in check_length
(key, len(self.parm_data[key]), length))
AmberError: FLAG LENNARD_JONES_14_ACOEF has 3160 elements; expected 1770
Exiting. All files have been retained.
File "/usr/local/amber16/bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
572, in loadcheck_prmtops
FILES.receptor_prmtop, FILES.ligand_prmtop)
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 98, in __init__
self.complex_prmtop = LoadParm(complex_prmtop)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/readparm.py",
line 66, in LoadParm
parm = parm.view_as(ChamberParm)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/amberformat.py",
line 420, in view_as
return cls.from_rawdata(self)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 259, in from_rawdata
inst.initialize_topology()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 103, in initialize_topology
AmberParm.initialize_topology(self, xyz, box)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 213, in initialize_topology
self.load_structure()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 143, in load_structure
super(ChamberParm, self).load_structure()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 498, in load_structure
self._check_section_lengths()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 423, in _check_section_lengths
check_length('LENNARD_JONES_14_ACOEF', ntypes*(ntypes+1)//2)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 407, in check_length
(key, len(self.parm_data[key]), length))
AmberError: FLAG LENNARD_JONES_14_ACOEF has 3160 elements; expected 1770
Exiting. All files have been retained.
File "/usr/local/amber16/bin/MMPBSA.py", line 98, in <module>
app.loadcheck_prmtops()
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
572, in loadcheck_prmtops
FILES.receptor_prmtop, FILES.ligand_prmtop)
File
"/usr/local/amber16/lib/python2.7/site-packages/MMPBSA_mods/parm_setup.py",
line 98, in __init__
self.complex_prmtop = LoadParm(complex_prmtop)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/readparm.py",
line 66, in LoadParm
parm = parm.view_as(ChamberParm)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/amberformat.py",
line 420, in view_as
return cls.from_rawdata(self)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 259, in from_rawdata
inst.initialize_topology()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 103, in initialize_topology
AmberParm.initialize_topology(self, xyz, box)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 213, in initialize_topology
self.load_structure()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 143, in load_structure
super(ChamberParm, self).load_structure()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_amberparm.py",
line 498, in load_structure
self._check_section_lengths()
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 423, in _check_section_lengths
check_length('LENNARD_JONES_14_ACOEF', ntypes*(ntypes+1)//2)
File
"/usr/local/amber16/lib/python2.7/site-packages/parmed/amber/_chamberparm.py",
line 407, in check_length
(key, len(self.parm_data[key]), length))
AmberError: FLAG LENNARD_JONES_14_ACOEF has 3160 elements; expected 1770
Exiting. All files have been retained.
So I am at an utter loss now and was wondering if you all can point out
where I went wrong. I know the lipid 17 library just came out but I do not
want to run these similations again if it can not be helped.
I am not sure if my attached files will show up for you through google
drive but if not I can email them to you or reply in the thread the
entirety of what anyone asks for.
complex.parm7
<
https://drive.google.com/file/d/0ByQ2En8MXKVSNlZuQUJaeTd3NWc/view?usp=drive_web>
complex.pdb
<
https://drive.google.com/file/d/0ByQ2En8MXKVSWkowb3pNSGNmV28/view?usp=drive_web>
complex.prmtop
<
https://drive.google.com/file/d/0ByQ2En8MXKVScGVuUXVBTmRRdVU/view?usp=drive_web>
ligand.parm7
<
https://drive.google.com/file/d/0ByQ2En8MXKVSZTg1U2dkWXdhQm8/view?usp=drive_web>
ligand.pdb
<
https://drive.google.com/file/d/0ByQ2En8MXKVSX1Y0NFpncjY3Wnc/view?usp=drive_web>
ligand.prmtop
<
https://drive.google.com/file/d/0ByQ2En8MXKVSXzJKVi1QTHVWeTQ/view?usp=drive_web>
receptor.parm7
<
https://drive.google.com/file/d/0ByQ2En8MXKVSUFJObGt3QW5semM/view?usp=drive_web>
receptor.prmtop
<
https://drive.google.com/file/d/0ByQ2En8MXKVSbDRUdkhkT2drX3c/view?usp=drive_web>
recptor.pdb
<
https://drive.google.com/file/d/0ByQ2En8MXKVSMTU4eEgwQ0NBNUk/view?usp=drive_web>
step5_charmm2amber.parm7
<
https://drive.google.com/file/d/0ByQ2En8MXKVSaUF6YkRNNVBxWWM/view?usp=drive_web>
step5_charmm2amber.pdb
<
https://drive.google.com/file/d/0ByQ2En8MXKVSeU8xdUpQOTlDZ0U/view?usp=drive_web>
Miguel Rivera
miguelrivera1855.gmail.com
Thanks!
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Received on Fri Apr 28 2017 - 15:30:02 PDT
