1. There are a significant number of overlaps. I didn't fully appreciate
that.
2. the first step of the MD gives ***** even if I start the temp at 0 and
raise it to 3K with dt=0.00001, and shake off and
I will keep minimizing...
On Wed, Apr 24, 2013 at 4:32 PM, Jonathan Gough
<jonathan.d.gough.gmail.com>wrote:
> Very helpful, thank you!
>
> So, if I understand this correctly, checkoverlap (using the default of
> 0.95) should not produce any results. additionally, I need to double check
> that there aren't any H's too close to the phosphates.
>
>
> On Wed, Apr 24, 2013 at 2:20 PM, David A Case <case.biomaps.rutgers.edu>wrote:
>
>> On Wed, Apr 24, 2013, Jonathan Gough wrote:
>> >
>>
>> > I didn't mention before, but will now (as I believe this is the REAL
>> issue)
>> > There are phosphates on a few residues.
>>
>> Check to see if you have hydrogens somewhere that are getting very close
>> to
>> the phosphate oxygens. For example, stop the MD simulation before the
>> ****
>> start to appear, and use the checkoverlap command to look for close
>> contacts.
>>
>> Many hydrogens in Amber force fields have zero van der Walls radius, and
>> can
>> get too close to phosphate groups. Of course, this is just a
>> guess...there
>> might be some other type of bad overlap that is leading to this behavior.
>> Finding out what is going on is the first step towards a fix.
>>
>> ...dac
>>
>>
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>>
>
>
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Received on Wed Apr 24 2013 - 14:30:04 PDT
