Re: [AMBER] question on how to keep the protein coordinate when adding solvateoct in xleap

From: v <xiaoli19871216.gmail.com>
Date: Wed, 15 Jan 2014 21:56:18 -0800

Hi, Kevin:
   The leap log is posted as below. There 8720 atoms in reference1.pdb.
After I saved the reference.pdb file, I found the coordinates of the
protein atoms didn't match the original one. I use vi to look at it.
Thanks a lot!
Li



> source leaprc.ff99SB
----- Source: /home/zhengshl/amber12_clean/
dat/leap/cmd/leaprc.ff99SB
----- Source of /home/zhengshl/amber12_clean/dat/leap/cmd/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters: /home/zhengshl/amber12_clean/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters: /home/zhengshl/amber12_clean/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /home/zhengshl/amber12_clean/dat/leap/lib/all_nucleic94.lib
Loading library: /home/zhengshl/amber12_clean/dat/leap/lib/all_amino94.lib
Loading library: /home/zhengshl/amber12_clean/dat/leap/lib/all_aminoct94.lib
Loading library: /home/zhengshl/amber12_clean/dat/leap/lib/all_aminont94.lib
Loading library: /home/zhengshl/amber12_clean/dat/leap/lib/ions94.lib
Loading library: /home/zhengshl/amber12_clean/dat/leap/lib/solvents.lib
> prot = loadpdb "reference1.pdb"
Loading PDB file: ./reference1.pdb
  total atoms in file: 8720
> set default nocenter on
> solvateoct prot TIP3PBOX 12.0
Scaling up box by a factor of 1.255061 to meet diagonal cut criterion
  Solute vdw bounding box: 69.478 103.715 52.311
  Total bounding box for atom centers: 133.836 133.836 133.836
      (box expansion for 'iso' is 118.2%)
  Solvent unit box: 18.774 18.774 18.774
  Volume: 1225713.857 A^3 (oct)
  Total mass 675848.382 amu, Density 0.916 g/cc
  Added 33943 residues.
> addions prot Na+ 0
25 Na+ ions required to neutralize.
Adding 25 counter ions to "prot" using 1A grid
Grid extends from solute vdw + 5.53 to 11.63
Resolution: 1.00 Angstrom.
grid build: 0 sec
Solvent present: replacing closest with ion
     when steric overlaps occur
Calculating grid charges
charges: 17 sec
(Replacing solvent molecule)
Placed Na+ in prot at (-21.22, 4.42, -9.62).
(Replacing solvent molecule)
Placed Na+ in prot at (-9.20, 11.70, -20.17).
(Replacing solvent molecule)
Placed Na+ in prot at (-26.68, 19.60, -6.85).
(Replacing solvent molecule)
Placed Na+ in prot at (-41.19, 21.79, 0.52).
(Replacing solvent molecule)
Placed Na+ in prot at (4.70, 16.43, -7.06).
(Replacing solvent molecule)
Placed Na+ in prot at (-40.13, 15.14, 11.12).
(Replacing solvent molecule)
Placed Na+ in prot at (-13.28, -1.54, -37.24).
(Replacing solvent molecule)
Placed Na+ in prot at (19.05, 10.84, -23.09).
(Replacing solvent molecule)
Placed Na+ in prot at (-2.00, 18.40, -25.85).
(Replacing solvent molecule)
Placed Na+ in prot at (-45.90, 29.65, 20.28).
(Replacing solvent molecule)
Placed Na+ in prot at (-22.90, 26.41, -2.11).
(Replacing solvent molecule)
Placed Na+ in prot at (-17.23, -14.05, -10.60).
(Replacing solvent molecule)
Placed Na+ in prot at (-14.92, 6.37, -14.64).
(Replacing solvent molecule)
Placed Na+ in prot at (-33.74, 34.08, 11.16).
(Replacing solvent molecule)
Placed Na+ in prot at (-50.89, 10.81, 17.10).
(Replacing solvent molecule)
Placed Na+ in prot at (5.55, 21.08, -14.08).
(Replacing solvent molecule)
Placed Na+ in prot at (-22.76, -16.18, -23.07).
(Replacing solvent molecule)
Placed Na+ in prot at (-19.07, 16.89, 32.90).
(Replacing solvent molecule)
Placed Na+ in prot at (-36.53, 32.25, -3.80).
(Replacing solvent molecule)
Placed Na+ in prot at (-6.60, 0.52, -43.64).
(Replacing solvent molecule)
Placed Na+ in prot at (-47.39, 15.43, 30.08).
(Replacing solvent molecule)
Placed Na+ in prot at (-14.92, 29.74, -14.26).
(Replacing solvent molecule)
Placed Na+ in prot at (32.60, -26.37, -20.84).
(Replacing solvent molecule)
Placed Na+ in prot at (-51.34, 21.77, 3.87).
(Replacing solvent molecule)
Placed Na+ in prot at (-21.96, -10.47, -35.32).

Done adding ions.
> savepdb prot reference.pdb
Writing pdb file: reference.pdb
 Converting N-terminal residue name to PDB format: NASN -> ASN
 Converting C-terminal residue name to PDB format: CPHE -> PHE


On Wed, Jan 15, 2014 at 7:07 PM, Kevin Hauser <84hauser.gmail.com> wrote:

> Hi Li,
>
> Can you post your leap.log, please? How many atoms is your
> "reference1.pdb"? And just to be clear, the actual coordinates of the atoms
> in reference1.pdb are different from those printed by leap, right? It's not
> that VMD has zoomed out since your system is much larger now, right?
>
> Kevin
>
>
> On Wed, Jan 15, 2014 at 6:24 PM, v <xiaoli19871216.gmail.com> wrote:
>
> > It still shows the change of the position of protein.
> > Thank you
> > Li
> >
> >
> > On Wed, Jan 15, 2014 at 3:17 PM, Jio M <jiomm.yahoo.com> wrote:
> >
> > > Hi Li,
> > >
> > > > source leaprc.ff99SB
> > > > prot = loadpdb "reference1.pdb"
> > > > addions prot Na+ 0
> > > > set default nocenter on
> > > > solvateoct prot TIP3PBOX 12.0
> > > > savepdb prot reference.pdb
> > >
> > >
> > > a vague thingy, try adding ions after water?
> > > solvateoct prot TIP3PBOX 12.0
> > >
> > > addions prot Na+ 0
> > >
> > >
> > >
> > >
> > > On Wednesday, January 15, 2014 10:54 PM, v <xiaoli19871216.gmail.com>
> > > wrote:
> > >
> > > I changed to another computer which have this option so there is no
> error
> > > message this time. But I still have that issue when using the
> solvatebox
> > > since the position of the protein is changed.
> > > Thank you
> > > Li
> > >
> > >
> > > On Wed, Jan 15, 2014 at 2:04 PM, David A Case <
> case.biomaps.rutgers.edu
> > > >wrote:
> > >
> > > > On Wed, Jan 15, 2014, v wrote:
> > > >
> > > > > > > set default nocenter on
> > > > > > > can't parse nocenter
> > > >
> > > > It looks like you need to update your version of AmberTools. Go to
> > > > $AMBERHOME and re-run the configure script, then type "make install"
> > > >
> > > > ...dac
> > > >
> > > > _______________________________________________
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> > > >
> > >
> > >
> > >
> > > --
> > > Li Xiao
> > > University of California, Irvine
> > > Email: xiaoli19871216.gmail.com
> > >
> > > _______________________________________________
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> > >
> >
> >
> >
> > --
> > Li Xiao
> > University of California, Irvine
> > Email: xiaoli19871216.gmail.com
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -- - -
> HK
>
>
>
> Kevin E. Hauser, Ph.D. Candidate
> NRSA Fellow, National Institutes of Health
> Carlos Simmerling Laboratory
> Miguel Garcia-Diaz Laboratory
> 100 Laufer Center for Physical and Quantitative Biology
> Stony Brook, New York 11794-5252
> Phone: (631) 632.5394 Email: 84hauser.gmail.com
>
>
>
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-- 
Li Xiao
University of California, Irvine
Email: xiaoli19871216.gmail.com


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Received on Wed Jan 15 2014 - 22:00:02 PST
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