AMBER Archive (2006)

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

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Thu Feb 02 2006 - 13:50:54 CST

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_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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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>
>
>
>
>
>
>
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-- 
                            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_at_qtp.ufl.edu
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