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

Erik Marklund erikm at xray.bmc.uu.se
Wed Apr 27 09:33:08 CEST 2011

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.


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/

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