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,
--
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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
er...@xray.bmc.uu.se http://folding.bmc.uu.se/
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