Hi All,
I am calculating PB energies of a DNA having a sequence, say
(GTAXCTC)2 by using amber-9 and MMPBSA.pl script. Here X is a modified
nucleotide. I can extract snapshots for ligand
(here it is X). However, I have problem in extracting snapshots for
receptor. The receptor here will be (GTA+CTC i.e. GTACTC)2. My problem
is as X is not situated at the end of DNA, I can
not create snapshots for(GTACTC)2.My MM-PBSA script is
-------------------------------------
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 190,227-828
-------------------------------------
In the above script 1-190 refers to GTA while 227-828 refers to CTC.
The script is only taking 1-190 as the receptor and leaves 227-828.
Will any body suggest me how to define the receptor here in the script?
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Received on Mon Mar 21 2011 - 04:30:04 PDT
