You just need to define two Receptor groups. For example:
NUMBER_LIG_GROUPS 1
LSTART 2622
LSTOP 3862
NUMBER_REC_GROUPS 2
RSTART 1
RSTOP 262
RSTART 3863
RSTOP 3864
Placing a '2' after NUMBER_REC_GROUPS defines two receptor groups, and then
you can define the atom numbers associated with the metals using the second
set of RSTART/RSTOP (I used atoms 3863 and 3864 as a guess since I didn't
know their respective numbers in your system).
Good luck!
-Bill
On Mon, Nov 8, 2010 at 4:24 AM, xuemeiwang1103 <xuemeiwang1103.163.com>wrote:
> Dear All :
> Recently,I began to calculate the binding free energy by using the
> MMPBSA meathod.But when I prepared the .prmtop file I meet the
> problem.Following the MMPBSA tutorial , the script :
> .........
> NUMBER_LIG_GROUPS 1
> LSTART 2622
> LSTOP 3862
> NUMBER_REC_GROUPS 1
> RSTART 1
> RSTOP 262
> .............
> In this script, I kown"RSTART 1 RSTOP 262" means the receptor is from
> atom 1 to 262. But consedering my system, there are two meatal ions, the
> protein is from residues 1 to 500, the ligand number is 501, then followned
> two ions(residues 502 and 503). I want to treat the protein and the meatal
> ions as the receptor, How could I deal with this if the number is not
> consecutive ? Thank you very much!
>
>
>
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Mon Nov 08 2010 - 04:00:03 PST
