Hello,
I am running per residue based energy calculations using idecomp commend
with sander instead of MMPBSA. Here is one of my input files:
&cntrl
imin = 1,
ncyc = 1,
maxcyc = 1,
igb = 5, saltcon=0.2,
ntb = 0,
cut = 999.0,
idecomp = 3,
/
Residues considered as REC
RRES 1 370
END
Residues considered as LIG
LRES 371 374
END
Residues to print
RES 1 374
END
END
When I use idecomp to decompose free energy of my system, the amber does
not recognize RRES and LRES card for the receptor and ligand in my system
as in the output file it shows:
LOADING THE DECOMP ATOMS AS GROUPS
----- READING GROUP 1; TITLE:
Residues considered as REC
Number of atoms in this group = 0
----- READING GROUP 2; TITLE:
Residues considered as LIG
Number of atoms in this group = 0
----- READING GROUP 3; TITLE:
Residues to print
GRP 3 RES 1 TO 374
Number of atoms in this group = 5803
----- END OF GROUP READ -----
However, it is confusing that the energy decomposition calculation was
still processed as TDC SDC BDC results were obtained in the output file.
The output is always like this with trials using different version of
AMBER. Can anybody confirm is this normal output for these residue cards or
anything wrong in my input file? Would this neglect the calculation of
interaction energies between the receptor and ligand?
Many Thanks!!
WenJuan
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Received on Fri Jan 18 2013 - 13:00:03 PST
