[gmx-users] Placing anion/cation at a particular distance from peptide

[Erik Marklund]

Mark Abraham skrev 2011-04-27 03.01:
> On 4/27/2011 5:13 AM, shivangi nangia wrote:
>> Dear gmx users,
>>
>> I need to design a starting configuration of a polypeptide with 
>> charged side chains sitting in a box of water with Cl- ions within 7 
>> ang of its radius.
>>
>> I realize that in such a system like charges will essentially prefer 
>> to be as far as possible from each other, but I still need the above 
>> stated configuration.
>>
>> Is there an easy way to specify the distance of the anions to be 
>> added from the peptide ?
>
> No. You will have to find water molecules a suitable distance from 
> your solute and replace them by hand (and update your .top accordingly).
>
> Mark
>
>
>
I can't think of why you would need such a configuration, and the 
clorides will quickly diffuse away. Nevertheless, here's what I would do:

* Use trjorder to order the water molecules according to their distance 
to the solute.
* Find one water molecule that is ~7 Å from the solute.
* Replace water molecules that (in the sequece of molecules in the 
ordered gro/pdf file) are near the water found to be at the correct 
distance with clorides.

Cheers,

-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/