AMBER Archive (2009)

Subject: Re: [AMBER] ambpdb problem

From: Ashish Runthala (ashish.runthala_at_gmail.com)
Date: Thu Jul 30 2009 - 22:44:10 CDT

Yeah Jordan is absolutely correct about that. you can get the charges.
But invivo system protein confirmations in native form dont have
charges, as it increases entropy of the system. So neutralize the
charge and then attempt a simulation,
Ashish

On Fri, Jul 31, 2009 at 4:32 AM, Jordan Monnet<monnet.jordan_at_free.fr> wrote:
> Hello,
>
>> 1) is there any option to get charges on the atoms as the structure so seen donot have
>> any charges... i.e. the pdb formatt. can the prmtop file be used to generate the charges
>
> You might want pqr instead of pdb?
>
> ambpdb -pqr -p prmtop < rst > whatever.pqr
>
> You will have charges and it really looks like a pdb file...
>
> }><(({*>
> __/
>
> Jordan MONNET
> Bachelor in Biology & Computer science
> University of Paris Diderot (Paris VII)
> Phone: +336 20 70 24 93
>
> http://monnet.jordan.free.fr/
>
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> 

-- 
Ashish Runthala,
Faculty Division III,
Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA

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