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.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.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.scripps.edu
> > [mailto:owner-amber.scripps.edu] On Behalf Of
> Varsha Goyal
> > Sent: Wednesday, February 01, 2006 19:00
> > To: amber.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
> >
>
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>
>
>
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Received on Fri Feb 03 2006 - 06:10:08 PST
