On a side-note, as long as the system that you define as your "Ligand" is a
series of continuous residues (which yours IS, if ligand is just protein2),
then MMPBSA.py will set all of this up for you. It may be worth trying that
version, found on
http://ambermd.org/tutorials/advanced/tutorial3/py_script. If you're
just getting started with MM/PBSA calculations, it is most
likely easier to use, and it catches more errors.
Good luck,
Jason
On Wed, Dec 8, 2010 at 11:43 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> My comments are below:
>
> On Wed, Dec 8, 2010 at 11:38 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
>>
>> Dear Sir/Madam,
>>
>> I have to calculate the MM/GBSA binding energy for a
>> protein1-protein2-protein3 complex. My prmtop files are listed in the order
>> of protein1, protein2 and then protein3.
>>
>> I want to calculate the binding energy of protein2 to the binary complex
>> of protein 1 and protein3. Since protein 1 and protein3 are separated, I
>> cannot define them as one. I have used the following input file for
>> snapshot.in, but how can I define if the receptor is separated into two
>> groups? What's wrong with my input file? Pls kindly instruct. Thank you.
>>
>> .GENERAL
>> PREFIX snapshot
>> PATH ./
>> COMPLEX 1
>> RECEPTOR 1
>> LIGAND 1
>> COMPT ./protein1protein2protein3.prmtop
>> RECPT ./protein1protein3.prmtop
>> LIGPT ./protein2.prmtop
>> GC 1
>> AS 0
>> DC 0
>> MM 0
>> GB 0
>> PB 0
>> MS 0
>> NM 0
>> .MAKECRD
>> BOX YES
>> NTOTAL 108188
>> NSTART 1
>> NSTOP 50000
>> NFREQ 50
>> NUMBER_LIG_GROUPS 2
>> LSTART 1
>> LSTOP 7864
>> LSTART 11204
>> LSTOP 12146
>>
>
> It looks like you have swapped LIG and REC here. REC has 2 groups
> (protein1 and protein3) and LIG only has 1 (protein2), right?
>
>
>> NUMBER_REC_GROUPS 1
>> RSTART 7865
>> RSTOP 11203
>> .TRAJECTORY
>> xxxx.mdcrd.gz
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Dec 08 2010 - 09:00:08 PST
