are you sure you defined the disulfide bond in leap? it isn't automatic.
On Tue, Sep 28, 2010 at 6:55 AM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> also, check if your minimization has insanely high vdw clashes at step 0,
> either ********* or some ~7 digit number. This would indicate that leap
> did not form the SS bond as planned.
>
> Thomas
>
> On Tue, September 28, 2010 5:51 am, Hannes Loeffler wrote:
>> On Tue, 28 Sep 2010 15:06:44 +0530
>> hirdesh kumar <hirdeshs8.gmail.com> wrote:
>>
>>> Hi,
>>> But I don't know the how to check the connection between S-S in the
>>> minimized structure.
>>
>> Write a restart file with 'ntwr' in your input file for minimisation and
>> then load it together with the topology file into vmd as I have
>> described in my previous email or with File->New Molecule... from the
>> menu. I guess pymol can do something similar.
>>
>>
>>> I *want to keep the S-S bond intact during minimization* so that it
>>> does not break. Is there any way for the same.
>>
>> The AMBER force fields do not allow bonds to break. If the
>> disulfide bond is properly defined but you still get an unnatural
>> elongation then your problem is somewhere else.
>>
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>>
>
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Tue Sep 28 2010 - 04:00:06 PDT
