I’m jumping in this one as I have a similar situation.
Following the suggested procedure (i.e. "A + B - (AB) will give you the buried area”) for:
1. dimer (no ligands) and
2. dimer plus ligands
and assuming that 2 > 1, would it be legitimate to assume that the difference in buried area is due to the ligands?
In the affirmative is there a way to validate this?
Thanks in advance for your suggestions
Regards
George
> On 21 Aug 2015, at 20:36, David A Case <david.case.rutgers.edu> wrote:
>
> On Fri, Aug 21, 2015, anu chandra wrote:
>>
>> trajin dimer.pdb # here, solvent and ions are removed beforehand
>> molsurf proteinA :1-290 1.out
>>
>> trajin proteinA.pdb # here, proteinB is removed from dimer.pdb
>> molsurf out 2.dat
>>
>>
>> Unfortunately, in both case the SASA of protein A looks exactly same.
>
> No, this is expected. Using the ":1-290" mask asks molsurf to just compute
> the area of those residues.
>
> If you want the buried surface area, load the dimer.pdb file, and do three
> molsurf calculations: one with :1-290, one with :291-end, and one with
> everything. A + B - (AB) will give you the buried area.
>
>
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Received on Mon Aug 24 2015 - 09:30:03 PDT
