Thank you，Kevin.
Li
On Sun, Jan 19, 2014 at 10:11 PM, Kevin Hauser <84hauser.gmail.com> wrote:
> Hi Li,
>
> The issue seems to be, at least in my trial of nocenter, that solvating the
> system mandates centering of coordinates, which is probably a smart thing
> to do for writing down coordinates during MD. If I don't solvate the
> system, this works for me.
>
> A quick grep'ing of the leap source files didn't get me far fast and I'm a
> bit busy to spend too much time sorting this out for you. I'd recommend
> first deciding whether this is the only solution to your problem - is this
> important for your MD or your analysis? If the latter, then check out
> cpptraj.
>
> Hope this helps,
> Kevin
>
>
>
>
> On Thu, Jan 16, 2014 at 12:56 AM, 肖立 <xiaoli19871216.gmail.com> wrote:
>
> > 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, 肖立 <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, 肖立 <
> > 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, 肖立 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
> > > > > >
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Li Xiao
> > > > > University of California, Irvine
> > > > > Email: xiaoli19871216.gmail.com
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
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> > > > > _______________________________________________
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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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> > >
> >
> ******************************************************************************
> > >
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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
> ════════════════════════════════════════════
>
>
> ******************************************************************************
> This e- mail message, including any attachments,
> is for the sole use of the intended recipient(s) and may
> contain confidential and privileged information.
> Any unauthorized review, use, disclosure or distribution is prohibited.
> If you are not the intended recipient, please contact the sender
> by e-mail and destroy all copies of the original.
>
> ******************************************************************************
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Li Xiao
University of California, Irvine
Email: xiaoli19871216.gmail.com
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Received on Mon Jan 20 2014 - 16:00:03 PST
