Re: [gmx-users] to add counter ions based on potential

[David van der Spoel]

Jochen Hub wrote:

sarbani chattopadhyay wrote:
  
Hi everybody,

I want to add counter ions based on potential and not 
randomly.
I will be very grateful if anyone can guide me through the command "genion" for 
this.


As far as I know, that has not been implemented yet. It is a good idea,
though.


It has been implemented but it has been broken for more than five years 
now :(.


Jochen




I tried with "-random no" but it didn't work.

Thanks in advance
Sarbani




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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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Re: [gmx-users] to add counter ions based on potential

[Allen Smith]

In message <[EMAIL PROTECTED]> (on 12 September 2008 15:25:38 +0200),
[EMAIL PROTECTED] (Jochen Hub) wrote:
>sarbani chattopadhyay wrote:
>>   
>> Hi everybody,
>> I want to add counter ions based on potential and not randomly.
>> I will be very grateful if anyone can guide me through the command
>>"genion" for this.
>
>As far as I know, that has not been implemented yet. It is a good idea,
>though.

I've written a perl program to do this for a limited case (addition of +1
ions only, just with respect to proteins and NADPH (NDP), based on whole
charges); see http://cesario.rutgers.edu/easmith/research/ (under the perl
programs) for check.water.for.pos.ions.pl. This program actually takes a PDB
file with waters added - see add.water.for.ions.pl for one program with an
example in it for how to do this; the "editconf" mention in it is because
it's preferable to do this with a centered protein. It then tells you the
best places to replace oxygens from water with positive ions; you can then
translate the PDB file back into gromacs format (ideally after adding
hydrogens again with something like the Richardsons' "reduce" program).

  -Allen

-- 
Allen Smith, Ph.D.http://cesario.rutgers.edu/easmith/
February 1, 2003   Space Shuttle Columbia
Ad Astra Per Aspera To The Stars Through Asperity
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Re: [gmx-users] to add counter ions based on potential

[Jochen Hub]

sarbani chattopadhyay wrote:
>   
> Hi everybody,
> I want to add counter ions based on potential and not 
> randomly.
> I will be very grateful if anyone can guide me through the command "genion" 
> for this.

As far as I know, that has not been implemented yet. It is a good idea,
though.

Jochen



> 
> I tried with "-random no" but it didn't work.
> 
> Thanks in advance
> Sarbani
> 
> 
> 
> 
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-- 

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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Re: [gmx-users] to add counter ions based on potential

[Justin A. Lemkul]

sarbani chattopadhyay wrote:
 
Hi everybody,
I want to add counter ions based on potential and 
not randomly.
I will be very grateful if anyone can guide me through the command 
"genion" for this.


I tried with "-random no" but it didn't work.


According to genion -h, you should use genion -norandom

-Justin



Thanks in advance
Sarbani



IN 






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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] to add counter ions based on potential

[sarbani chattopadhyay]

  
Hi everybody,
I want to add counter ions based on potential and not 
randomly.
I will be very grateful if anyone can guide me through the command "genion" for 
this.

I tried with "-random no" but it didn't work.

Thanks in advance
Sarbani___
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