The proper command (I think) should be
ambpdb -pqr -p prmtop < inpcrd > pdb
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.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
>>>
> --------------------------------------------------------------
>>> ---------
>>> The AMBER Mail Reflector
>>> To post, send mail to amber.scripps.edu
>>> To unsubscribe, send "unsubscribe amber" to
>> majordomo.scripps.edu
>>
>>
> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber.scripps.edu
>> To unsubscribe, send "unsubscribe amber" to
>> majordomo.scripps.edu
>>
>
>
>
>
>
>
>
> __________________________________________________________
> Find your next car at http://autos.yahoo.ca
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project and Department of Chemistry
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
============================================================================
To announce that there must be no criticism of the president,
or that we are to stand by the president right or wrong,
is not only unpatriotic and servile, but is morally treasonable
to the American public."
-- Theodore Roosevelt
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Feb 03 2006 - 06:10:08 PST
