AMBER Archive (2006)

Subject: RE: AMBER: Charges on atoms in protein :AMBER

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Feb 02 2006 - 14:14:53 CST

Dear Varsha,

If u want to write the charges in the .pdb file, u need to set the
pdbwritecharges option on in xleap, and then save it, as follows;

...
set default PdbWriteCharges on
savepdb molecule molecule.pdb
...

The molecule.pdb file's last column is going to have the charge info. Now,
which program can be used to see these charges... GRASP definitely can
load the structure with the charge info given at the last column. Or in
xleap, if u 'edit molecule', this will show the charges, too. I am not
sure, but InsigthII might show the charges, too. In any case, if u need to
charges in the .pdb file, u need to set the above PdbWriteCharges option
on before saving the structure in a .pdb file.

Best,

On Thu, 2 Feb 2006, Varsha Goyal wrote:

> Dear Ross,
> I did what you have said but still i don't see any
> charges. Also there are no charges in pdb file itself.
> But when i look at charge section in prmtop file, it
> looks like this
>
> %FLAG CHARGE
>
> %FORMAT(5E16.8)
>
> 2.04636429E+00 -6.67300626E+00 2.04636429E+00
> 2.04636429E+00 1.08823576E+01
> -1.03484442E+01 -7.57501011E+00 4.95464337E+00
> 3.42579240E-01 1.60538463E+00
> -8.41870260E-01 7.32536460E-01 7.32536460E-01
> -4.84713180E-01 -6.94451853E+00
> 6.64931727E+00 3.74832711E+00 2.53654416E+00
> -1.04359112E+01 2.35432116E+00
> 2.09009781E+00 1.08841798E+01 -1.03484442E+01
> -7.57501011E+00 4.95464337E+00
> -5.01113250E-01 2.04636429E+00 -9.11115000E-02
> 6.17735970E-01 6.17735970E-01
> -2.57845545E+00 -2.98481274E+00 3.75743826E+00
> -6.22838214E+00 6.21744876E+00
> 2.51467740E+00 -4.73962023E+00 2.86454556E+00
> -2.06640882E+00 2.58209991E+00
> -3.59343756E+00 2.63676681E+00 -4.34966301E+00
> 3.09779100E+00 2.26503189E+00
> 1.08841798E+01 -1.03484442E+01 -7.57501011E+00
> 4.95464337E+00 -4.59201960E-01
> 1.27191654E+00 1.27191654E+00 1.08841798E+01
> -1.03484442E+01 -7.57501011E+00
> 4.95464337E+00 -2.55112200E-02 1.59627348E+00
> -2.76978960E-01 5.37557850E-01
> 5.37557850E-01 -2.00445300E-02 -3.47317038E+00
> 3.09596877E+00 -4.26584043E+00
> 3.01761288E+00 5.87851398E+00 -1.01662212E+01
> 7.27434216E+00 -4.26584043E+00
> 3.01761288E+00 -3.47317038E+00 3.09596877E+00
> 1.08841798E+01 -1.03484442E+01
> -7.57501011E+00 4.95464337E+00 -4.59201960E-01
> 1.27191654E+00 1.27191654E+00
> 1.08841798E+01 -1.03484442E+01 -6.33953817E+00
> 5.00566581E+00 -4.37335200E+00
> 2.59849998E+00 -1.71289620E-01 6.59647260E-01
> 6.59647260E-01 3.40757010E-01
> 1.87689690E-01 1.87689690E-01 -8.72848170E-01
> 1.13160483E+00 1.13160483E+00
> -2.60578890E-01 2.06823105E+00 2.06823105E+00
> -7.02287442E+00 6.19558200E+00
> 6.19558200E+00 6.19558200E+00 1.33769904E+01
> -1.07402236E+01 -7.57501011E+00
> 4.95464337E+00 3.42579240E-01 1.60538463E+00
> -8.41870260E-01 7.32536460E-01
> 7.32536460E-01 -4.84713180E-01 -6.94451853E+00
> 6.64931727E+00 3.74832711E+00
>
> Is it possible that sybyl is not displaying charges??
> Is there any other software in whihc i can look at
> charges on specific atoms?
> I tried VMD but i don;t see any option to display
> charge on particular atom.
>
> Thanks i advance,
> Varsha
> --- Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
> > Dear Varsha,
> >
> > Take a look at the CHARGE section of the prmtop file
> > and see if there are
> > lots of atoms with zero charge. I doubt this is the
> > problem though, the
> > charge on the TIP3P waters is defined in the library
> > file used by leap.
> > Similarly the library files you loaded for HIC etc
> > should contain charges.
> >
> > More likely leap just doesn't write the charges to
> > the pdb file, I assume
> > this is what you are loading into Sybyl, not the
> > prmtop and inpcrd file.
> >
> > Try creating a pdb file that includes the charges
> > using ambpdb
> >
> > ambpdb -pqr prmtop < inpcrd > pdb
> >
> > Then take a look at it again in Sybyl.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | Department of Molecular Biology TPC15 |
> > | The Scripps Research Institute |
> > | Tel: +1 858 784 8889 | EMail:-
> > ross_at_rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on
> > request |
> >
> > Note: Electronic Mail is not secure, has no
> > guarantee of delivery, may not
> > be read every day, and should not be used for urgent
> > or sensitive issues.
> >
> > > -----Original Message-----
> > > From: owner-amber_at_scripps.edu
> > > [mailto:owner-amber_at_scripps.edu] On Behalf Of
> > Varsha Goyal
> > > Sent: Wednesday, February 01, 2006 19:00
> > > To: amber_at_scripps.edu
> > > Subject: AMBER: Charges on atoms in protein :AMBER
> >
> > >
> > > Hello,
> > > I generated pdb file after runnig leap:
> > >
> > > My leap.in is
> > >
> > > source leaprc.gaff
> > > source leaprc.ff99
> > > loadoff ZNC.lib
> > > loadoff HIC.lib
> > > loadoff HIF.lib
> > > loadoff wat.lib
> > > loadAmberParams frcmod.caii
> > > loadAmberParams frcmod.znc
> > > loadAmberParams ligand.frcmod
> > > loadAmberprep HIC.in
> > > loadAmberprep wat.in
> > > loadAmberprep ligand.prepin
> > > loadAmberprep HIF.in
> > > set BZO restype protein
> > > set ZNC restype protein
> > > set HIC restype protein
> > > set HIF restype protein
> > > Prot = loadPdb protein.pdb
> > > charge Prot
> > > addions Prot K+ 1
> > > solvateBox Prot TIP3PBOX 12 iso
> > > saveAmberParm Prot prmtop.top prmcrd.crd
> > > savepdb Prot protein-mod.pdb
> > > check Prot
> > > charge Prot
> > >
> > >
> > > But when i look at structure in Sybyl7.1 and try
> > to
> > > display charge on residues i see 0.0 charge on
> > every
> > > single atom. Does amber assign charge by itself or
> > do
> > > we assign charges to residues before running leap.
> >
> > >
> > > Thanks in advance,
> > > Varsha Gupta
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> >
> __________________________________________________________
> >
> > > Find your next car at http://autos.yahoo.ca
> > >
> >
> --------------------------------------------------------------
> > > ---------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber_at_scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to
> > majordomo_at_scripps.edu
> > >
> >
> >
> >
> -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to
> > majordomo_at_scripps.edu
> >
>
>
>
>
>
>
>
> __________________________________________________________
> Find your next car at http://autos.yahoo.ca
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu