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

From: Kevin Hauser <84hauser.gmail.com>
Date: Mon, 20 Jan 2014 01:11:08 -0500

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
> > > > >
> > > > > _______________________________________________
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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
> > > _______________________________________________
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> > >
> >
> >
> >
> > --
> > -- - -
> > 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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>


-- 
-- - -
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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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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Received on Sun Jan 19 2014 - 22:30:02 PST
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