Hi,
You may want to try the 'makestructure' command in cpptraj (V13),
which allows you to adjust various dihedral angle types for a
specified residue range. For example, to apply phi/psi of -57/-47 to
residues 3-7:
makestructure custom:3-7:-57:-47
See the manual for full details of the command.
-Dan
On Sun, May 12, 2013 at 11:05 PM, sandeep singh
<sandysingh.imtech.res.in> wrote:
>
> Using impose command in tleap, I want to impose phi, psi torsion angles of a
> protein which is 500 residues long, but it seems tleap can handle proteins with
> only 248 residues.
>
> Even if I am using sequence (and not imposing torsion angles) then also tleap is
> not able to handle protein with more than 248 residues.
>
> I am using following input file for tleap
>
> input file for tleap (249 residues)
> ########################################################
> source /opt/softwares/amber9/dat/leap/cmd/leaprc.ff99SB
> input1=sequence { PRO VAL PHE ALA GLN GLN ASN TYR ALA ASN PRO ARG GLU ALA ASN
> GLY ARG ILE VAL CYS ALA ASN CYS HIS LEU ALA GLN LYS ALA VAL GLU ILE GLU VAL PRO
> GLN ALA VAL LEU PRO ASP THR VAL PHE GLU ALA VAL ILE GLU LEU PRO TYR ASP LYS GLN
> VAL LYS GLN VAL LEU ALA ASN GLY LYS LYS GLY ASP LEU ASN VAL GLY MET VAL LEU ILE
> LEU PRO GLU GLY PHE GLU LEU ALA PRO PRO ASP ARG VAL PRO ALA GLU ILE LYS GLU LYS
> VAL GLY ASN LEU TYR TYR GLN PRO TYR SER PRO GLU GLN LYS ASN ILE LEU VAL VAL GLY
> PRO VAL PRO GLY LYS LYS TYR SER GLU MET VAL VAL PRO ILE LEU SER PRO ASP PRO ALA
> LYS ASN LYS ASN VAL SER TYR LEU LYS TYR PRO ILE TYR PHE GLY GLY GLN ARG GLY ARG
> GLY GLN VAL TYR PRO ASP GLY LYS LYS SER ASN ASN THR ILE TYR ASN ALA SER ALA ALA
> GLY LYS ILE VAL ALA ILE THR ALA LEU SER GLU LYS LYS GLY GLY PHE GLU VAL SER ILE
> GLU LYS ALA ASN GLY GLU VAL VAL VAL ASP LYS ILE PRO ALA GLY PRO ASP LEU ILE VAL
> LYS GLU GLY GLN THR VAL GLN ALA ASP GLN PRO LEU THR ASN ASN PRO ASN VAL GLY GLY
> PHE GLY GLN ALA GLU THR GLU ILE VAL LEU GLN ASN PRO ALA }
> savePdb input1 1e2vA.pdb
> quit
> ########################################################
>
>
> comand to execute tleap
> /opt/softwares/amber11/exe/tleap -f inputfile
>
> tleap output after executing it
> ########################################
> -I: Adding /opt/softwares/amber9/dat/leap/prep to search path.
> -I: Adding /opt/softwares/amber9/dat/leap/lib to search path.
> -I: Adding /opt/softwares/amber9/dat/leap/parm to search path.
> -I: Adding /opt/softwares/amber9/dat/leap/cmd to search path.
> -f: Source 1e2vA.main.7531.input.
>
> Welcome to LEaP!
> (no leaprc in search path)
> Sourcing: ./1e2vA.main.7531.input
> ----- Source: /opt/softwares/amber9/dat/leap/cmd/leaprc.ff99SB
> ----- Source of /opt/softwares/amber9/dat/leap/cmd/leaprc.ff99SB done Log file:
> ./leap.log
> Loading parameters: /opt/softwares/amber9/dat/leap/parm/parm99.dat Reading title:
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
> Loading parameters: /opt/softwares/amber9/dat/leap/parm/frcmod.ff99SB Reading
> force field modification type file (frcmod)
> Reading title:
> Modification/update of parm99.dat (Hornak & Simmerling)
> Loading library: /opt/softwares/amber9/dat/leap/lib/all_nucleic94.lib Loading
> library: /opt/softwares/amber9/dat/leap/lib/all_amino94.lib Loading library:
> /opt/softwares/amber9/dat/leap/lib/all_aminoct94.lib Loading library:
> /opt/softwares/amber9/dat/leap/lib/all_aminont94.lib Loading library:
> /opt/softwares/amber9/dat/leap/lib/ions94.lib
> Loading library: /opt/softwares/amber9/dat/leap/lib/solvents.lib
> Segmentation fault
> ########################################
>
>
>
> When I am using sequence length of 248 residues ( removing last ALA from
> inputfile above) then pdb file is made but still "Segmentation fault" message
> comes
>
> input file for tleap (248 residues i.e. last ALA removed)
> ########################################################
> source /opt/softwares/amber9/dat/leap/cmd/leaprc.ff99SB
> input1=sequence { PRO VAL PHE ALA GLN GLN ASN TYR ALA ASN PRO ARG GLU ALA ASN
> GLY ARG ILE VAL CYS ALA ASN CYS HIS LEU ALA GLN LYS ALA VAL GLU ILE GLU VAL PRO
> GLN ALA VAL LEU PRO ASP THR VAL PHE GLU ALA VAL ILE GLU LEU PRO TYR ASP LYS GLN
> VAL LYS GLN VAL LEU ALA ASN GLY LYS LYS GLY ASP LEU ASN VAL GLY MET VAL LEU ILE
> LEU PRO GLU GLY PHE GLU LEU ALA PRO PRO ASP ARG VAL PRO ALA GLU ILE LYS GLU LYS
> VAL GLY ASN LEU TYR TYR GLN PRO TYR SER PRO GLU GLN LYS ASN ILE LEU VAL VAL GLY
> PRO VAL PRO GLY LYS LYS TYR SER GLU MET VAL VAL PRO ILE LEU SER PRO ASP PRO ALA
> LYS ASN LYS ASN VAL SER TYR LEU LYS TYR PRO ILE TYR PHE GLY GLY GLN ARG GLY ARG
> GLY GLN VAL TYR PRO ASP GLY LYS LYS SER ASN ASN THR ILE TYR ASN ALA SER ALA ALA
> GLY LYS ILE VAL ALA ILE THR ALA LEU SER GLU LYS LYS GLY GLY PHE GLU VAL SER ILE
> GLU LYS ALA ASN GLY GLU VAL VAL VAL ASP LYS ILE PRO ALA GLY PRO ASP LEU ILE VAL
> LYS GLU GLY GLN THR VAL GLN ALA ASP GLN PRO LEU THR ASN ASN PRO ASN VAL GLY GLY
> PHE GLY GLN ALA GLU THR GLU ILE VAL LEU GLN ASN PRO }
> savePdb input1 1e2vA.pdb
> quit
> ########################################################
>
>
>
>
>
> log file for 248 residues input file
>
> ##############################################
> -I: Adding /opt/softwares/amber9/dat/leap/prep to search path.
> -I: Adding /opt/softwares/amber9/dat/leap/lib to search path.
> -I: Adding /opt/softwares/amber9/dat/leap/parm to search path.
> -I: Adding /opt/softwares/amber9/dat/leap/cmd to search path.
> -f: Source 1e2vA.main.7531.input-1.
>
> Welcome to LEaP!
> (no leaprc in search path)
> Sourcing: ./1e2vA.main.7531.input-1
> ----- Source: /opt/softwares/amber9/dat/leap/cmd/leaprc.ff99SB
> ----- Source of /opt/softwares/amber9/dat/leap/cmd/leaprc.ff99SB done Log file:
> ./leap.log
> Loading parameters: /opt/softwares/amber9/dat/leap/parm/parm99.dat Reading title:
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
> Loading parameters: /opt/softwares/amber9/dat/leap/parm/frcmod.ff99SB Reading
> force field modification type file (frcmod)
> Reading title:
> Modification/update of parm99.dat (Hornak & Simmerling)
> Loading library: /opt/softwares/amber9/dat/leap/lib/all_nucleic94.lib Loading
> library: /opt/softwares/amber9/dat/leap/lib/all_amino94.lib Loading library:
> /opt/softwares/amber9/dat/leap/lib/all_aminoct94.lib Loading library:
> /opt/softwares/amber9/dat/leap/lib/all_aminont94.lib Loading library:
> /opt/softwares/amber9/dat/leap/lib/ions94.lib
> Loading library: /opt/softwares/amber9/dat/leap/lib/solvents.lib
> Writing pdb file: 1e2vA.pdb
> Quit
> Segmentation fault
> ###############################################
>
>
>
> kindly help me to solve it, as many of my proteins are 500+ residues long
>
>
>
>
> --
> Sandeep Singh
>
>
>
>
> ______________________________________________________________________
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue May 14 2013 - 08:00:02 PDT
