No, it didn t work. So the option is to indeed use some bond and dihedral stiff temrs as you ve saied, however charges and force values still need to be calculated or taken from previous works.
Best regards,
Andrew
14.01.2010, 10:54, "Ross Walker" <ross.rosswalker.co.uk>:
> Hi Andrew,
>
>> šI actually wonder that if Zn is bound but not ion, probably it can
>> šinfluence geometry of the whole protein if I parametrize it as an ion.
>> šProbably I should šfix Zn residue and amino acid residues which are
>> šbound to it. I think it is reasonable.
>
> This is very much a try it and see situation. I would start by just doing a
> 2+ ion and see what happens. Note fixing the surrounding residues may not be
> as easy as it appears at first since really you need to fix them with
> respect to each other and the zinc ion rather than to a fixed starting
> structure. You could always add bond, angle and dihedral terms that are
> sufficiently stiff to accomplish the same type of restraints.
>
> Good luck,
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
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Received on Wed Oct 26 2011 - 06:00:04 PDT
