On Wed, May 05, 2010, Homa Azizian wrote:
> I have problem in minimizing my system protein+nonstandard residue in
> it.always The my system stop at the same step. and this is the result
> from the out file, It seems that the EEL option decrease dramaticly. I
> check the whole structure using check command in xleap but nothing
> is unusual with that. my non-standard residue in this system hase a
> phosphate -O-P-O(OH) {charged -1}group with one oxygen protonated. Also
> I had a system which the phosphate has the charge -2, and this system
> minimize well.
It is easy to end up with a protonated phosphate model where there are no van
der Waals terms on the H atom, and where that hydrogen can then get
arbitrarily close to some other oxygen. Check the structure just before
you get the large negative EEL values and look for close contacts.
...good luck...dac
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Received on Wed May 05 2010 - 05:00:04 PDT
