Premalatha,
This could be an effect of magnesium ions being problematic for fixed charge atom force fields. This issue was discussed in a fairly recent paper on alternative magnesium atom models, particularly when two magnesium are close to each other, see:
http://dx.doi.org/10.1016/j.jmb.2006.10.095
I would also recommend you take a look at this recent paper discussing new magnesium parameters:
http://dx.doi.org/10.1021/ct400177g
Best,
Jesper
On Aug 12, 2013, at 9:10 AM, David A Case <case.biomaps.rutgers.edu> wrote:
> On Mon, Aug 12, 2013, Mallipeddi, Premalatha wrote:
>>
>> The main issue is, the metals start to move away from each
>> other.
>
> This could happen for all sorts of reasons. People on the list have no idea
> what geometry you are looking at, what the coordination of the metal atoms is,
> and so on. Hence they cannot be of much help.
>
>>
>> I tried MG2 this time in desc
>>> desc MG2.1
>> RESIDUE name: MG2
>> RESIDUE sequence number: 1
>> RESIDUE PDB sequence number: 0
>> Type: undefined
>> Connection atoms:
>> Improper torsions:
>> Contents:
>> A<MG 1>
>>
>> Where am I going wrong?
>
> Nowhere...above looks correct. It shows you that the is one atom (named "MG")
> in the first residue of the unit "MG2". Follow this by "desc MG2.1.MG", and
> you will find the charge on that atom (which is 2.)
>
> ...dac
>
>
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Received on Mon Aug 12 2013 - 15:00:02 PDT
