Hi amber developers,
I tried to use sleap to build topologies for my protein-ligand-complex in three ways.
Maybe this is interesting for sleap developers.
And maybe someone can tell me how to set this task up right.
regards,
Oliver
### Trial 1 - reading and parameterizing the receptor and ligand separately and using 'combine' to build the complex
oak.debian:~/experiment/sleap/1hxb$ sleap
[gtkleap]$ source leaprc.ff03.r1
[gtkleap]$ source leaprc.gaff
[gtkleap]$
[gtkleap]$ set default fastbld on
[gtkleap]$
[gtkleap]$ rec = loadpdb rec.pdb
[gtkleap]$ saveamberparm rec rec.top rec.crd
[gtkleap]$
[gtkleap]$ lig = loadpdb lig.pdb
Warning: when building by model, can not find model in library
Warning: I am trying to handle it by myself under following steps
Warning: (1) fix bond order automatically
Warning: (2) add hydrogens
Warning: (3) call antechamber to setup partial charge and atom type
Warning: (4) call parmchk to add missing force field parameters
step 1. fixbo done
step 2. add H done
Total number of electrons: 360; net charge: 0
Running: /usr/local/amber10/bin/mopac.sh
step 3. set charge and type
Running parmchk to get extra force field parameters
step 4. parmchk done
Warning: I was managable to fix bond order and add hydrogens
Warning: according to its geometrical configuration,but I still
Warning: suggest you to take a look at the residue. It is saved
Warning: as fragment.mol2 under you working directory.
[gtkleap]$ savemol2 lig lig.mol2
[gtkleap]$ saveamberparm lig lig.top lig.crd
[gtkleap]$ wat = loadpdb wat.pdb
[gtkleap]$ com = combine{rec lig}
Sequence: rec
Sequence: lig
[gtkleap]$ saveamberparm com com.top com.crd
Error: can't find parameter for bond C-HA
[gtkleap]$
### Trial 2 - reading and parameterizing the complex from one pdb
oak.debian:~/experiment/sleap/1hxb$ sleap
[gtkleap]$ source leaprc.ff03.r1
[gtkleap]$ source leaprc.gaff
[gtkleap]$
[gtkleap]$ set default fastbld on
[gtkleap]$
[gtkleap]$ com = loadpdb com.pdb
Warning: when building by model, can not find model in library
Warning: I am trying to handle it by myself under following steps
Warning: (1) fix bond order automatically
Warning: (2) add hydrogens
Warning: (3) call antechamber to setup partial charge and atom type
Warning: (4) call parmchk to add missing force field parameters
step 1. fixbo done
step 2. add H done
Total number of electrons: 360; net charge: 0
Running: /usr/local/amber10/bin/mopac.sh
step 3. set charge and type
Running parmchk to get extra force field parameters
step 4. parmchk done
Warning: I was managable to fix bond order and add hydrogens
Warning: according to its geometrical configuration,but I still
Warning: suggest you to take a look at the residue. It is saved
Warning: as fragment.mol2 under you working directory.
[gtkleap]$ saveamberparm com com.top com.crd
[gtkleap]$ savepdb com com.protonated.pdb
saving com to com.protonated.pdb
[gtkleap]$ addions Cl- 0
sleap: ../freelib/boost/shared_ptr.hpp:247: typename boost::detail::shared_ptr_traits<T>::reference boost::shared_ptr<T>::operator*() const [with T = mort::molecule_t]: Assertion `px != 0' failed.
Abgebrochen
### Trial 3 - using sleap to parameterize the ligand and save a mol2, using tleap to read the mol2 and proceed
oak.debian:~/experiment/sleap/1hxb$ sleap
[gtkleap]$ source leaprc.ff03.r1
[gtkleap]$ source leaprc.gaff
[gtkleap]$
[gtkleap]$ set default fastbld on
[gtkleap]$
[gtkleap]$ rec = loadpdb rec.pdb
[gtkleap]$ saveamberparm rec rec.top rec.crd
[gtkleap]$
[gtkleap]$ lig = loadpdb lig.pdb
Warning: when building by model, can not find model LIG in library
Warning: I am trying to handle it by myself under following steps
Warning: (1) fix bond order automatically
Warning: (2) add hydrogens
Warning: (3) call antechamber to setup partial charge and atom type
Warning: (4) call parmchk to add missing force field parameters
step 1. fixbo done
step 2. add H done
Total number of electrons: 360; net charge: 0
Running: /usr/local/amber10/bin/mopac.sh
step 3. set charge and type
Running parmchk to get extra force field parameters
step 4. parmchk done
Warning: I was managable to fix bond order and add hydrogens
Warning: according to its geometrical configuration,but I still
Warning: suggest you to take a look at the residue. It is saved
Warning: as fragment.mol2 under you working directory.
[gtkleap]$ savemol2 lig lig.mol2
[gtkleap]$ quit
oak.debian:~/experiment/sleap/1hxb$ tleap
-I: Adding /usr/local/amber10/dat/leap/prep to search path.
-I: Adding /usr/local/amber10/dat/leap/lib to search path.
-I: Adding /usr/local/amber10/dat/leap/parm to search path.
-I: Adding /usr/local/amber10/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
> set default echo on
can't parse echo
usage: set <container> <parameter> <object>
or: set default <parameter> <value>
> set default PdbWriteCharges "on"
>
> source leaprc.ff03.r1
----- Source: /usr/local/amber10/dat/leap/cmd/leaprc.ff03.r1
----- Source of /usr/local/amber10/dat/leap/cmd/leaprc.ff03.r1 done
Log file: ./leap.log
Loading parameters: /usr/local/amber10/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters: /usr/local/amber10/dat/leap/parm/frcmod.ff03
Reading force field modification type file (frcmod)
Reading title:
Duan et al ff03 phi psi torsions
Loading library: /usr/local/amber10/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber10/dat/leap/lib/solvents.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_aminoct03.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_aminont03.lib
Loading library: /usr/local/amber10/dat/leap/lib/all_amino03.lib
> source leaprc.gaff
----- Source: /usr/local/amber10/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/amber10/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/amber10/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
> lig = loadmol2 lig.mol2
Loading Mol2 file: ./lig.mol2
Reading MOLECULE named lig
/usr/local/amber10/bin/tleap: line 8: 16092 Speicherzugriffsfehler /usr/local/amber10/bin/teLeap -I/usr/local/amber10/dat/leap/prep -I/usr/local/amber10/dat/leap/lib -I/usr/local/amber10/dat/leap/parm -I/usr/local/amber10/dat/leap/cmd $*
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- application/download attachment: lig.pdb
- application/download attachment: rec.pdb
Received on Tue Nov 10 2009 - 02:00:02 PST
