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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 08 2010 - 09:00:05 PST
